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LongText Report for: 5D3Z-pdb

Name Class
5D3Z-pdb
HEADER    HYDROLASE/HYDROLASE INHIBITOR           06-AUG-15   5D3Z              
TITLE     CRYSTAL STRUCTURE OF THE THIOESTERASE DOMAIN OF DEOXYERYTHRONOLIDE B  
TITLE    2 SYNTHASE IN COMPLEX WITH A SMALL PHOSPHONATE INHIBITOR               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: ERYTHRONOLIDE SYNTHASE, MODULES 5 AND 6;                   
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UNP RESIDUES 2904-3172;                                    
COMPND   5 SYNONYM: 6-DEOXYERYTHRONOLIDE B SYNTHASE III,DEBS 3,ORF 3;           
COMPND   6 EC: 2.3.1.94;                                                        
COMPND   7 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: SACCHAROPOLYSPORA ERYTHRAEA;                    
SOURCE   3 ORGANISM_TAXID: 1836;                                                
SOURCE   4 GENE: ERYA;                                                          
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3;                                  
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PBACP                                     
KEYWDS    THIOESTERASE DOMAINE ALPHA / BETA HYDROLASE FOLD DEOXYERYTHRONOLIDE B 
KEYWDS   2 SYNTHASE ALLYL PHOSPHONATE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR  
KEYWDS   3 COMPLEX                                                              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    F.BERGERET,P.ARGYROPOULOS,C.N.BODDY,T.M.SCHMEING                      
REVDAT   1   09-DEC-15 5D3Z    0                                                
JRNL        AUTH   P.ARGYROPOULOS,F.BERGERET,C.PARDIN,J.M.REIMER,A.PINTO,       
JRNL        AUTH 2 C.N.BODDY,T.MARTIN SCHMEING                                  
JRNL        TITL   TOWARDS A CHARACTERIZATION OF THE STRUCTURAL DETERMINANTS OF 
JRNL        TITL 2 SPECIFICITY IN THE MACROCYCLIZING THIOESTERASE FOR           
JRNL        TITL 3 DEOXYERYTHRONOLIDE B BIOSYNTHESIS.                           
JRNL        REF    BIOCHIM.BIOPHYS.ACTA                       2015              
JRNL        REFN                   ISSN 0006-3002                               
JRNL        PMID   26592346                                                     
JRNL        DOI    10.1016/J.BBAGEN.2015.11.007                                 
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.10 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : REFMAC 5.8.0049                                      
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON                               
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 32.15                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 17518                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.171                           
REMARK   3   R VALUE            (WORKING SET) : 0.170                           
REMARK   3   FREE R VALUE                     : 0.190                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 932                             
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 20                           
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.10                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.16                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 1267                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 99.63                        
REMARK   3   BIN R VALUE           (WORKING SET) : 0.1540                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 73                           
REMARK   3   BIN FREE R VALUE                    : 0.1440                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 1964                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 21                                      
REMARK   3   SOLVENT ATOMS            : 209                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 17.47                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -0.09000                                             
REMARK   3    B22 (A**2) : -0.09000                                             
REMARK   3    B33 (A**2) : 0.30000                                              
REMARK   3    B12 (A**2) : -0.05000                                             
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.                                 
REMARK   3   ESU BASED ON R VALUE                            (A): 0.184         
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.145         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.090         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.298         
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.945                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.935                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2055 ; 0.007 ; 0.019       
REMARK   3   BOND LENGTHS OTHERS               (A):  1889 ; 0.001 ; 0.020       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  2807 ; 1.144 ; 1.961       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  4341 ; 0.757 ; 3.000       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   267 ; 4.902 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):    85 ;26.050 ;22.706       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   283 ;12.441 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    17 ;14.089 ;15.000       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   308 ; 0.059 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2362 ; 0.005 ; 0.021       
REMARK   3   GENERAL PLANES OTHERS             (A):   463 ; 0.001 ; 0.020       
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT      
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  1065 ; 0.877 ; 1.628       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  1064 ; 0.847 ; 1.626       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  1333 ; 1.476 ; 2.433       
REMARK   3   MAIN-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B REFINED ATOMS     (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B OTHER ATOMS       (A**2):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT       
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS STATISTICS                                           
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL                              
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED : MASK                                                 
REMARK   3   PARAMETERS FOR MASK CALCULATION                                    
REMARK   3   VDW PROBE RADIUS   : 1.20                                          
REMARK   3   ION PROBE RADIUS   : 0.80                                          
REMARK   3   SHRINKAGE RADIUS   : 0.80                                          
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING   
REMARK   3  POSITIONS U VALUES : REFINED INDIVIDUALLY                           
REMARK   4                                                                      
REMARK   4 5D3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-15.                  
REMARK 100 THE DEPOSITION ID IS D_1000212619.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 02-OCT-12                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 6.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU MICROMAX-007 HF             
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                             
REMARK 200  MONOCHROMATOR                  : RIGAKU VARIMAX-HF                  
REMARK 200  OPTICS                         : RIGAKU VARIMAX-HF                  
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU SATURN 944+                 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706                       
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000 706                       
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 18469                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.100                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 32.150                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.6                               
REMARK 200  DATA REDUNDANCY                : 10.50                              
REMARK 200  R MERGE                    (I) : 0.12000                            
REMARK 200  R SYM                      (I) : 0.12000                            
REMARK 200   FOR THE DATA SET  : 20.5000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.17                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.4                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 8.10                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.27000                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200   FOR SHELL         : 6.900                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER 2.5.1                                          
REMARK 200 STARTING MODEL: 1KEZ                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 54.74                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA-CACODYLATE, 35-38%             
REMARK 280  POLYETHYLENE GLYCOL (PEG) 300, 0.18-0.24 M CA-ACETATE, PH 6.5,      
REMARK 280  VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1                          
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z                                                
REMARK 290       3555   -X+Y,-X,Z                                               
REMARK 290       4555   Y,X,-Z                                                  
REMARK 290       5555   X-Y,-Y,-Z                                               
REMARK 290       6555   -X,-X+Y,-Z                                              
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   5  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   6 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   6 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     GLY A   174                                                      
REMARK 465     HIS A   175                                                      
REMARK 465     GLY A   280                                                      
REMARK 465     GLY A   281                                                      
REMARK 465     ASN A   282                                                      
REMARK 465     SER A   283                                                      
REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     GLU A  46    CD   OE1  OE2                                       
REMARK 470     ASP A  52    CG   OD1  OD2                                       
REMARK 470     GLU A  67    CG   CD   OE1  OE2                                  
REMARK 470     ARG A  87    CZ   NH1  NH2                                       
REMARK 470     LYS A 134    CG   CD   CE   NZ                                   
REMARK 470     ASP A 177    CG   OD1  OD2                                       
REMARK 470     ASP A 240    CG   OD1  OD2                                       
REMARK 470     LYS A 243    CE   NZ                                             
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   O    HOH A   407     O    HOH A   579              2.14            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500    SER A 142     -131.60     57.61                                   
REMARK 500    ASP A 239     -164.25   -127.98                                   
REMARK 500    GLN A 264      -80.81   -122.23                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 610                                                                      
REMARK 610 MISSING HETEROATOM                                                   
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 610 I=INSERTION CODE):                                                   
REMARK 610   M RES C SSEQI                                                      
REMARK 610     57H A  301                                                       
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              CA A 303  CA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASP A  49   OD2                                                    
REMARK 620 2 HOH A 416   O    99.0                                              
REMARK 620 3 HOH A 564   O    83.4  90.7                                        
REMARK 620 4 VAL A  27   O    46.8 143.1  97.1                                  
REMARK 620 5 HOH A 523   O    98.1 162.9  92.1  53.1                            
REMARK 620 N                    1     2     3     4                             
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue 57H A 301                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 302                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303                  
DBREF  5D3Z A   15   283  UNP    Q03133   ERYA3_SACER   2904   3172             
SEQRES   1 A  269  SER SER ALA LEU ARG ASP GLY TYR ARG GLN ALA GLY VAL          
SEQRES   2 A  269  SER GLY ARG VAL ARG SER TYR LEU ASP LEU LEU ALA GLY          
SEQRES   3 A  269  LEU SER ASP PHE ARG GLU HIS PHE ASP GLY SER ASP GLY          
SEQRES   4 A  269  PHE SER LEU ASP LEU VAL ASP MET ALA ASP GLY PRO GLY          
SEQRES   5 A  269  GLU VAL THR VAL ILE CYS CYS ALA GLY THR ALA ALA ILE          
SEQRES   6 A  269  SER GLY PRO HIS GLU PHE THR ARG LEU ALA GLY ALA LEU          
SEQRES   7 A  269  ARG GLY ILE ALA PRO VAL ARG ALA VAL PRO GLN PRO GLY          
SEQRES   8 A  269  TYR GLU GLU GLY GLU PRO LEU PRO SER SER MET ALA ALA          
SEQRES   9 A  269  VAL ALA ALA VAL GLN ALA ASP ALA VAL ILE ARG THR GLN          
SEQRES  10 A  269  GLY ASP LYS PRO PHE VAL VAL ALA GLY HIS SER ALA GLY          
SEQRES  11 A  269  ALA LEU MET ALA TYR ALA LEU ALA THR GLU LEU LEU ASP          
SEQRES  12 A  269  ARG GLY HIS PRO PRO ARG GLY VAL VAL LEU ILE ASP VAL          
SEQRES  13 A  269  TYR PRO PRO GLY HIS GLN ASP ALA MET ASN ALA TRP LEU          
SEQRES  14 A  269  GLU GLU LEU THR ALA THR LEU PHE ASP ARG GLU THR VAL          
SEQRES  15 A  269  ARG MET ASP ASP THR ARG LEU THR ALA LEU GLY ALA TYR          
SEQRES  16 A  269  ASP ARG LEU THR GLY GLN TRP ARG PRO ARG GLU THR GLY          
SEQRES  17 A  269  LEU PRO THR LEU LEU VAL SER ALA GLY GLU PRO MET GLY          
SEQRES  18 A  269  PRO TRP PRO ASP ASP SER TRP LYS PRO THR TRP PRO PHE          
SEQRES  19 A  269  GLU HIS ASP THR VAL ALA VAL PRO GLY ASP HIS PHE THR          
SEQRES  20 A  269  MET VAL GLN GLU HIS ALA ASP ALA ILE ALA ARG HIS ILE          
SEQRES  21 A  269  ASP ALA TRP LEU GLY GLY GLY ASN SER                          
HET    57H  A 301       4                                                       
HET    1PE  A 302      16                                                       
HET     CA  A 303       1                                                       
HETNAM     57H PROP-2-EN-1-YLPHOSPHONIC ACID                                    
HETNAM     1PE PENTAETHYLENE GLYCOL                                             
HETNAM      CA CALCIUM ION                                                      
HETSYN     1PE PEG400                                                           
FORMUL   2  57H    C3 H7 O3 P                                                   
FORMUL   3  1PE    C10 H22 O6                                                   
FORMUL   4   CA    CA 2+                                                        
FORMUL   5  HOH   *209(H2 O)                                                    
HELIX    1 AA1 SER A   16  SER A   28  1                                  13    
HELIX    2 AA2 ARG A   30  ASP A   43  1                                  14    
HELIX    3 AA3 GLY A   81  GLU A   84  5                                   4    
HELIX    4 AA4 PHE A   85  ARG A   93  1                                   9    
HELIX    5 AA5 SER A  115  GLY A  132  1                                  18    
HELIX    6 AA6 SER A  142  ARG A  158  1                                  17    
HELIX    7 AA7 ASP A  177  TRP A  182  1                                   6    
HELIX    8 AA8 TRP A  182  ARG A  193  1                                  12    
HELIX    9 AA9 ASP A  199  TRP A  216  1                                  18    
HELIX   10 AB1 PHE A  260  GLN A  264  5                                   5    
HELIX   11 AB2 HIS A  266  GLY A  279  1                                  14    
SHEET    1 AA1 2 HIS A  47  PHE A  48  0                                        
SHEET    2 AA1 2 LEU A 112  PRO A 113  1  O  LEU A 112   N  PHE A  48           
SHEET    1 AA2 7 VAL A  59  ALA A  62  0                                        
SHEET    2 AA2 7 VAL A  98  VAL A 101 -1  O  ALA A 100   N  VAL A  59           
SHEET    3 AA2 7 THR A  69  CYS A  73  1  N  CYS A  72   O  ARG A  99           
SHEET    4 AA2 7 PHE A 136  HIS A 141  1  O  ALA A 139   N  CYS A  73           
SHEET    5 AA2 7 GLY A 164  ILE A 168  1  O  ILE A 168   N  GLY A 140           
SHEET    6 AA2 7 THR A 225  ALA A 230  1  O  LEU A 226   N  VAL A 165           
SHEET    7 AA2 7 ASP A 251  VAL A 255  1  O  ASP A 251   N  LEU A 227           
LINK         OD2 ASP A  49                CA    CA A 303     1555   1555  2.15  
LINK         OG  SER A 142                 PAG 57H A 301     1555   1555  1.75  
LINK        CA    CA A 303                 O   HOH A 416     1555   1555  2.44  
LINK        CA    CA A 303                 O   HOH A 564     1555   1555  2.54  
LINK         O   VAL A  27                CA    CA A 303     1555   1554  2.26  
LINK        CA    CA A 303                 O   HOH A 523     1555   1556  2.17  
SITE     1 AC1  6 SER A 142  ALA A 143  HIS A 259  1PE A 302                    
SITE     2 AC1  6 HOH A 439  HOH A 539                                          
SITE     1 AC2  8 ILE A  79  HIS A  83  GLU A  84  HIS A 141                    
SITE     2 AC2  8 THR A 195  57H A 301  HOH A 404  HOH A 466                    
SITE     1 AC3  5 VAL A  27  ASP A  49  HOH A 416  HOH A 523                    
SITE     2 AC3  5 HOH A 564                                                     
CRYST1  112.544  112.544   42.780  90.00  90.00 120.00 P 3 2 1       6          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.008885  0.005130  0.000000        0.00000                         
SCALE2      0.000000  0.010260  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.023375        0.00000                         
TER    1983      GLY A 279                                                      
MASTER      333    0    3   11    9    0    6    6 2194    1   25   21          
END                                                                             

Send your questions or comments to :
Mail to: Nicolas Lenfant, Thierry Hotelier, Yves Bourne, Pascale Marchot and Arnaud Chatonnet.
Please cite: Lenfant 2013 Nucleic.Acids.Res. or Marchot Chatonnet 2012 Prot.Pept Lett.
For technical information about these pages see:
ESTHER Home Page and ACEDB Home Page
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