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HEADER HYDROLASE 06-AUG-15 5D3K
TITLE CRYSTAL STRUCTURE OF THE THIOESTERASE DOMAIN OF DEOXYERYTHRONOLIDE B
TITLE 2 SYNTHASE
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, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR F.BERGERET,P.ARGYROPOULOS,C.N.BODDY,T.M.SCHMEING
REVDAT 1 09-DEC-15 5D3K 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. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0073
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) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.96
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 32914
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) : 0.158
REMARK 3 R VALUE (WORKING SET) : 0.156
REMARK 3 FREE R VALUE : 0.187
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700
REMARK 3 FREE R VALUE TEST SET COUNT : 1638
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) : 1.70
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2436
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96
REMARK 3 BIN R VALUE (WORKING SET) : 0.2250
REMARK 3 BIN FREE R VALUE SET COUNT : 113
REMARK 3 BIN FREE R VALUE : 0.2470
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2006
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 32
REMARK 3 SOLVENT ATOMS : 224
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.05
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.01000
REMARK 3 B22 (A**2) : 0.01000
REMARK 3 B33 (A**2) : -0.04000
REMARK 3 B12 (A**2) : 0.01000
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): 0.084
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.758
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2101 ; 0.021 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1929 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2865 ; 1.995 ; 1.961
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4437 ; 0.964 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 5.395 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;26.522 ;22.778
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 285 ;12.589 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.645 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 310 ; 0.132 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2422 ; 0.012 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 478 ; 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): 1084 ; 1.765 ; 1.413
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1084 ; 1.759 ; 1.412
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1357 ; 2.577 ; 2.109
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 5D3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-15.
REMARK 100 THE DEPOSITION ID IS D_1000212609.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-FEB-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CLSI
REMARK 200 BEAMLINE : 08B1-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97957
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34562
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
REMARK 200 RESOLUTION RANGE LOW (A) : 36.960
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 4.100
REMARK 200 R MERGE (I) : 0.12000
REMARK 200 R SYM (I) : 0.12000
REMARK 200 FOR THE DATA SET : 7.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 4.00
REMARK 200 R MERGE FOR SHELL (I) : 0.47800
REMARK 200 R SYM FOR SHELL (I) : 0.06900
REMARK 200 FOR SHELL : 2.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: REFMAC 5.8.0073
REMARK 200 STARTING MODEL: 1KEZ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.24
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA-CACODYLATE, 35-38%
REMARK 280 POLYETHYLENE GLYCOL , 0.18-0.24 M CA-ACETATE, PEG300, 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 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 67 CG CD OE1 OE2
REMARK 470 GLU A 84 CG CD OE1 OE2
REMARK 470 LYS A 134 CG CD CE NZ
REMARK 470 GLU A 185 CG CD OE1 OE2
REMARK 470 LYS A 243 CE NZ
REMARK 470 SER A 283 O
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 612 O HOH A 613 1.69
REMARK 500 O HOH A 612 O HOH A 615 1.87
REMARK 500 O HOH A 437 O HOH A 570 1.89
REMARK 500 O HOH A 482 O HOH A 603 1.99
REMARK 500 O HOH A 401 O HOH A 529 2.03
REMARK 500 O HOH A 600 O HOH A 609 2.07
REMARK 500 O HOH A 408 O HOH A 425 2.12
REMARK 500 O HOH A 408 O HOH A 491 2.18
REMARK 500 O HOH A 489 O HOH A 497 2.18
REMARK 500 O HOH A 402 O HOH A 536 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU A 184 CD GLU A 184 OE1 0.082
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ASP A 49 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES
REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 ARG A 129 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 ARG A 158 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES
REMARK 500 ASP A 199 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ARG A 202 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 ARG A 211 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES
REMARK 500 ARG A 219 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 ARG A 219 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 ASP A 258 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES
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 -129.40 59.61
REMARK 500 GLN A 264 -85.10 -123.71
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 1PE A 302
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 411 O 105.8
REMARK 620 3 HOH A 568 O 83.0 92.2
REMARK 620 4 VAL A 27 O 41.0 141.3 99.9
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 304 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 108 OE2
REMARK 620 2 ASP A 199 OD2 108.1
REMARK 620 3 HOH A 500 O 78.4 172.9
REMARK 620 4 GLY A 279 O 84.4 39.5 141.2
REMARK 620 5 GLY A 281 O 86.6 36.1 144.6 3.5
REMARK 620 6 HOH A 540 O 84.8 86.5 97.1 115.9 113.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 305 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 275 OD1
REMARK 620 2 HOH A 469 O 78.9
REMARK 620 3 HOH A 446 O 68.6 147.0
REMARK 620 4 HOH A 459 O 99.7 89.8 90.0
REMARK 620 5 GLU A 107 OE1 56.2 74.2 82.9 44.5
REMARK 620 6 GLU A 107 OE2 53.9 74.3 81.8 46.6 2.3
REMARK 620 7 HOH A 575 O 93.4 94.6 92.9 166.8 148.7 146.6
REMARK 620 N 1 2 3 4 5 6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE 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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5D2R RELATED DB: PDB
DBREF 5D3K 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 1PE A 301 16
HET 1PE A 302 13
HET CA A 303 1
HET CA A 304 1
HET CA A 305 1
HETNAM 1PE PENTAETHYLENE GLYCOL
HETNAM CA CALCIUM ION
HETSYN 1PE PEG400
FORMUL 2 1PE 2(C10 H22 O6)
FORMUL 4 CA 3(CA 2+)
FORMUL 7 HOH *224(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 GLN A 176 TRP A 182 1 7
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 LEU A 167
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 2.27
LINK OE2 GLU A 108 CA CA A 304 1555 1555 2.08
LINK OD2 ASP A 199 CA CA A 304 1555 1555 2.34
LINK OD1 ASP A 275 CA CA A 305 1555 1555 2.36
LINK CA CA A 303 O HOH A 411 1555 1555 2.44
LINK CA CA A 303 O HOH A 568 1555 1555 2.34
LINK CA CA A 304 O HOH A 500 1555 1555 2.37
LINK CA CA A 305 O HOH A 469 1555 1555 2.34
LINK CA CA A 305 O HOH A 446 1555 1555 2.45
LINK CA CA A 305 O HOH A 459 1555 1555 2.33
LINK O VAL A 27 CA CA A 303 1555 1554 2.28
LINK OE1 GLU A 107 CA CA A 305 1555 2865 2.44
LINK OE2 GLU A 107 CA CA A 305 1555 2865 2.49
LINK O GLY A 279 CA CA A 304 1555 3785 2.36
LINK O GLY A 281 CA CA A 304 1555 3785 2.23
LINK CA CA A 304 O HOH A 540 1555 2865 2.47
LINK CA CA A 305 O HOH A 575 1555 3785 2.44
SITE 1 AC1 8 HIS A 83 ARG A 87 HIS A 141 THR A 195
SITE 2 AC1 8 HOH A 406 HOH A 536 HOH A 550 HOH A 566
SITE 1 AC2 9 TYR A 22 VAL A 31 GLN A 176 MET A 179
SITE 2 AC2 9 LEU A 183 THR A 187 ASP A 210 THR A 213
SITE 3 AC2 9 GLY A 214
SITE 1 AC3 4 VAL A 27 ASP A 49 HOH A 411 HOH A 568
SITE 1 AC4 3 GLU A 108 ASP A 199 HOH A 500
SITE 1 AC5 4 ASP A 275 HOH A 446 HOH A 459 HOH A 469
CRYST1 112.920 112.920 42.970 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 0.008856 0.005113 0.000000 0.00000
SCALE2 0.000000 0.010226 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023272 0.00000
TER 2019 SER A 283
MASTER 409 0 5 11 9 0 8 6 2262 1 42 21
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