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HEADER HYDROLASE 23-MAR-12 4AO7
TITLE ZINC BOUND STRUCTURE OF A NOVEL COLD-ADAPTED ESTERASE FROM AN ARCTIC
TITLE 2 INTERTIDAL METAGENOMIC LIBRARY
CAVEAT 4AO7 GLU A 40 C-ALPHA IS PLANAR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ESTERASE;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED;
SOURCE 3 ORGANISM_TAXID: 32644;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K-12;
SOURCE 7 EXPRESSION_SYSTEM_VARIANT: M15 (PREP4);
SOURCE 8 OTHER_DETAILS: FROM A METAGENOMIC LIBRARY FROM INTERTIDAL ZONE AT
SOURCE 9 SVALBARD ARCHIPELAGO
KEYWDS HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.FU,H.-K.S.LEIROS,D.D.PASCALE,K.A.JOHNSON,H.M.BLENCKE,B.LANDFALD
REVDAT 1 08-AUG-12 4AO7 0
JRNL AUTH J.FU,H.-K.S.LEIROS,D.DE PASCALE,K.A.JOHNSON,H.M.BLENCKE,
JRNL AUTH 2 B.LANDFALD
JRNL TITL FUNCTIONAL AND STRUCTURAL STUDIES OF A NOVEL COLD-ADAPTED
JRNL TITL 2 ESTERASE FROM AN ARCTIC INTERTIDAL METAGENOMIC LIBRARY.
JRNL REF APPL.MICROBIOL.BIOTECHNOL. 2012
JRNL REFN ESSN 1432-0614
JRNL PMID 22832985
JRNL DOI 10.1007/S00253-012-4276-9
REMARK 2
REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
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) : 1.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.49
REMARK 3 NUMBER OF REFLECTIONS : 17371
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) : 0.17860
REMARK 3 R VALUE (WORKING SET) : 0.17606
REMARK 3 FREE R VALUE : 0.22752
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1
REMARK 3 FREE R VALUE TEST SET COUNT : 939
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) : 1.850
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.898
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1217
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20
REMARK 3 BIN R VALUE (WORKING SET) : 0.256
REMARK 3 BIN FREE R VALUE SET COUNT : 75
REMARK 3 BIN FREE R VALUE : 0.353
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1764
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 3
REMARK 3 SOLVENT ATOMS : 123
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 33.5
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.269
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.39
REMARK 3 B22 (A**2) : -1.33
REMARK 3 B33 (A**2) : 0.93
REMARK 3 B12 (A**2) : 0.00
REMARK 3 B13 (A**2) : 0.00
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.144
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.656
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1768 ; 0.012 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 1199 ; 0.003 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2402 ; 1.344 ; 1.961
REMARK 3 BOND ANGLES OTHERS (DEGREES): 2916 ; 0.893 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 233 ; 5.435 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ;35.163 ;23.676
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 290 ;12.531 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;13.256 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 263 ; 0.083 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2003 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 354 ; 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): 1131 ; 0.802 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 477 ; 0.176 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1804 ; 1.440 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 637 ; 1.849 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 597 ; 2.876 ; 4.500
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 : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 5 A 247
REMARK 3 ORIGIN FOR THE GROUP (A): 35.4275 16.3534 15.0241
REMARK 3 T TENSOR
REMARK 3 T11: 0.0408 T22: 0.0446
REMARK 3 T33: 0.0432 T12: -0.0022
REMARK 3 T13: 0.0039 T23: -0.0050
REMARK 3 L TENSOR
REMARK 3 L11: 0.5455 L22: 1.5279
REMARK 3 L33: 0.5129 L12: 0.6618
REMARK 3 L13: 0.4497 L23: 0.2615
REMARK 3 S TENSOR
REMARK 3 S11: -0.1010 S12: -0.0694 S13: 0.0451
REMARK 3 S21: -0.1718 S22: 0.0075 S23: -0.0552
REMARK 3 S31: -0.0828 S32: -0.0654 S33: 0.0934
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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
REMARK 3 RIDING POSITIONS.
REMARK 4
REMARK 4 4AO7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAR-12.
REMARK 100 THE PDBE ID CODE IS EBI-51839.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID29
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.282
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34844
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.85
REMARK 200 RESOLUTION RANGE LOW (A) : 54.00
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 6.5
REMARK 200 R MERGE (I) : 0.05
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 0.00
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5
REMARK 200 DATA REDUNDANCY IN SHELL : 5.7
REMARK 200 R MERGE FOR SHELL (I) : 0.72
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 0.00
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
REMARK 200 SOFTWARE USED: SHELXC, D AND E
REMARK 200 STARTING MODEL: NONE
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.61
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X+1/2,Y+1/2,-Z
REMARK 290 4555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 27.83000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.01500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.83000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.01500
REMARK 290 SMTRY3 4 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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2040 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 18500 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -179.9 KCAL/MOL
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 350 BIOMT1 2 -1.000000 0.000000 0.000000 55.66000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 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 MET A -11
REMARK 465 ARG A -10
REMARK 465 GLY A -9
REMARK 465 SER A -8
REMARK 465 HIS A -7
REMARK 465 HIS A -6
REMARK 465 HIS A -5
REMARK 465 HIS A -4
REMARK 465 HIS A -3
REMARK 465 HIS A -2
REMARK 465 GLY A -1
REMARK 465 SER A 0
REMARK 465 MET A 1
REMARK 465 ARG A 2
REMARK 465 HIS A 3
REMARK 465 GLN A 4
REMARK 465 GLY A 53
REMARK 465 THR A 54
REMARK 465 THR A 55
REMARK 465 HIS A 56
REMARK 465 LYS A 57
REMARK 465 LYS A 58
REMARK 465 VAL A 59
REMARK 465 HIS A 84
REMARK 465 GLY A 85
REMARK 465 GLU A 86
REMARK 465 ARG A 87
REMARK 465 ALA A 88
REMARK 465 SER A 89
REMARK 465 VAL A 90
REMARK 465 GLN A 91
REMARK 465 ALA A 92
REMARK 465 GLY A 93
REMARK 465 ARG A 94
REMARK 465 GLU A 95
REMARK 465 PRO A 96
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 ASP A 11 CG OD1 OD2
REMARK 480 GLU A 12 CB CG CD OE1 OE2
REMARK 480 ARG A 13 CA CB CG CD NE CZ NH1 NH2
REMARK 480 LYS A 14 C O
REMARK 480 ASP A 27 OD1
REMARK 480 GLU A 40 CB CG CD OE1 OE2
REMARK 480 SER A 42 OG
REMARK 480 TYR A 61 CE2
REMARK 480 PRO A 82 O
REMARK 480 ARG A 107 CG CD NE CZ NH1 NH2
REMARK 480 GLU A 111 CD OE1 OE2
REMARK 480 GLU A 171 OE2
REMARK 480 GLU A 176 OE2
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 N MET A 5 O HOH A 2001 2.09
REMARK 500 OE1B GLN A 216 O HOH A 2078 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 2084 O HOH A 2084 2655 1.37
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 ASP A 11 CB ASP A 11 CG -0.335
REMARK 500 GLU A 12 CA GLU A 12 CB 0.837
REMARK 500 ARG A 13 CA ARG A 13 C -0.358
REMARK 500 ARG A 13 N ARG A 13 CA 0.126
REMARK 500 LYS A 14 CA LYS A 14 C 0.542
REMARK 500 ASP A 27 CG ASP A 27 OD1 0.394
REMARK 500 TYR A 61 CD2 TYR A 61 CE2 -0.286
REMARK 500 TYR A 61 CE2 TYR A 61 CZ 0.188
REMARK 500 PRO A 82 C PRO A 82 O -0.188
REMARK 500 ARG A 107 CB ARG A 107 CG -0.165
REMARK 500 GLU A 111 CG GLU A 111 CD -0.248
REMARK 500 GLU A 171 CD GLU A 171 OE2 -0.205
REMARK 500 GLU A 176 CD GLU A 176 OE2 0.368
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 11 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES
REMARK 500 GLU A 12 CB - CA - C ANGL. DEV. = -34.9 DEGREES
REMARK 500 GLU A 12 N - CA - CB ANGL. DEV. = -23.5 DEGREES
REMARK 500 ARG A 13 CA - C - O ANGL. DEV. = -34.1 DEGREES
REMARK 500 ARG A 13 CB - CA - C ANGL. DEV. = -28.4 DEGREES
REMARK 500 ARG A 13 N - CA - C ANGL. DEV. = 29.4 DEGREES
REMARK 500 ARG A 13 N - CA - CB ANGL. DEV. = 13.7 DEGREES
REMARK 500 ARG A 13 CA - C - N ANGL. DEV. = 33.4 DEGREES
REMARK 500 ASP A 27 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES
REMARK 500 GLU A 40 CB - CA - C ANGL. DEV. = 35.6 DEGREES
REMARK 500 TYR A 61 CE1 - CZ - CE2 ANGL. DEV. = -11.7 DEGREES
REMARK 500 TYR A 61 CZ - CE2 - CD2 ANGL. DEV. = 9.3 DEGREES
REMARK 500 GLU A 171 CG - CD - OE2 ANGL. DEV. = 15.1 DEGREES
REMARK 500 GLU A 171 OE1 - CD - OE2 ANGL. DEV. = -34.2 DEGREES
REMARK 500 GLU A 176 OE1 - CD - OE2 ANGL. DEV. = -22.3 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 ASN A 8 124.44 145.38
REMARK 500 ARG A 13 -60.88 -10.82
REMARK 500 PRO A 82 54.98 -61.75
REMARK 500 SER A 144 -115.71 65.38
REMARK 500 GLN A 216 58.39 -95.89
REMARK 500 PHE A 235 -87.83 -99.27
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLU A 12 ARG A 13 122.76
REMARK 500 ARG A 13 LYS A 14 148.00
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ASP A 27 0.08 SIDE CHAIN
REMARK 500 GLU A 171 0.13 SIDE CHAIN
REMARK 500 GLU A 176 0.21 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 ARG A 13 16.2 L L OUTSIDE RANGE
REMARK 500 GLU A 40 5.1 L L EXPECTING SP3
REMARK 500
REMARK 500 REMARK: NULL
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 ZN A1248 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 233 OE1
REMARK 620 2 GLU A 233 OE2 64.2
REMARK 620 3 HOH A2081 O 131.9 87.7
REMARK 620 4 HOH A2109 O 86.1 140.4 94.6
REMARK 620 5 HIS A 220 ND1 111.1 99.4 111.4 116.1
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1249 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 51 NE2
REMARK 620 2 HOH A2018 O 108.7
REMARK 620 3 HOH A2019 O 91.2 107.3
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1250 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 198 OE2
REMARK 620 2 HOH A2076 O 101.5
REMARK 620 3 HOH A2097 O 133.0 84.0
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1248
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1249
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1250
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4AO6 RELATED DB: PDB
REMARK 900 NATIVE STRUCTURE OF A NOVEL COLD-ADAPTED ESTERASE FROM
REMARK 900 AN ARCTIC INTERTIDAL METAGENOMIC LIBRARY
REMARK 900 RELATED ID: 4AO8 RELATED DB: PDB
REMARK 900 PEG-BOUND COMPLEX OF A NOVEL COLD-ADAPTED ESTERASE
REMARK 900 FROM AN ARCTIC INTERTIDAL METAGENOMIC LIBRARY
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RESIDUES MRGSHHHHHHGS ARE THE N-TERMINAL HIS TAG
DBREF 4AO7 A 1 247 PDB 4AO7 4AO7 1 247
SEQADV 4AO7 MET A -11 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 ARG A -10 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 GLY A -9 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 SER A -8 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 HIS A -7 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 HIS A -6 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 HIS A -5 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 HIS A -4 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 HIS A -3 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 HIS A -2 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 GLY A -1 PDB 4AO7 EXPRESSION TAG
SEQADV 4AO7 SER A 0 PDB 4AO7 EXPRESSION TAG
SEQRES 1 A 259 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET
SEQRES 2 A 259 ARG HIS GLN MET SER TRP ASN GLY LYS ASP GLU ARG LYS
SEQRES 3 A 259 LEU SER VAL GLN GLU ARG GLY PHE SER LEU GLU VAL ASP
SEQRES 4 A 259 GLY ARG THR VAL PRO GLY VAL TYR TRP SER PRO ALA GLU
SEQRES 5 A 259 GLY SER SER ASP ARG LEU VAL LEU LEU GLY HIS GLY GLY
SEQRES 6 A 259 THR THR HIS LYS LYS VAL GLU TYR ILE GLU GLN VAL ALA
SEQRES 7 A 259 LYS LEU LEU VAL GLY ARG GLY ILE SER ALA MET ALA ILE
SEQRES 8 A 259 ASP GLY PRO GLY HIS GLY GLU ARG ALA SER VAL GLN ALA
SEQRES 9 A 259 GLY ARG GLU PRO THR ASP VAL VAL GLY LEU ASP ALA PHE
SEQRES 10 A 259 PRO ARG MET TRP HIS GLU GLY GLY GLY THR ALA ALA VAL
SEQRES 11 A 259 ILE ALA ASP TRP ALA ALA ALA LEU ASP PHE ILE GLU ALA
SEQRES 12 A 259 GLU GLU GLY PRO ARG PRO THR GLY TRP TRP GLY LEU SER
SEQRES 13 A 259 MET GLY THR MET MET GLY LEU PRO VAL THR ALA SER ASP
SEQRES 14 A 259 LYS ARG ILE LYS VAL ALA LEU LEU GLY LEU MET GLY VAL
SEQRES 15 A 259 GLU GLY VAL ASN GLY GLU ASP LEU VAL ARG LEU ALA PRO
SEQRES 16 A 259 GLN VAL THR CYS PRO VAL ARG TYR LEU LEU GLN TRP ASP
SEQRES 17 A 259 ASP GLU LEU VAL SER LEU GLN SER GLY LEU GLU LEU PHE
SEQRES 18 A 259 GLY LYS LEU GLY THR LYS GLN LYS THR LEU HIS VAL ASN
SEQRES 19 A 259 PRO GLY LYS HIS SER ALA VAL PRO THR TRP GLU MET PHE
SEQRES 20 A 259 ALA GLY THR VAL ASP TYR LEU ASP GLN ARG LEU LYS
HET ZN A1248 1
HET ZN A1249 1
HET ZN A1250 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 3(ZN 2+)
FORMUL 3 HOH *123(H2 O)
HELIX 1 1 GLU A 60 ARG A 72 1 13
HELIX 2 2 ASP A 98 LEU A 102 5 5
HELIX 3 3 ALA A 104 GLY A 112 1 9
HELIX 4 4 GLY A 113 GLY A 134 1 22
HELIX 5 5 SER A 144 ASP A 157 1 14
HELIX 6 6 ASN A 174 ALA A 182 1 9
HELIX 7 7 PRO A 183 VAL A 185 5 3
HELIX 8 8 SER A 201 LEU A 212 1 12
HELIX 9 9 PRO A 230 PHE A 235 1 6
HELIX 10 10 PHE A 235 LEU A 246 1 12
SHEET 1 AA 9 SER A 6 TRP A 7 0
SHEET 2 AA 9 VAL A 17 VAL A 26 -1 O SER A 23 N SER A 6
SHEET 3 AA 9 ARG A 29 PRO A 38 -1 O ARG A 29 N VAL A 26
SHEET 4 AA 9 ILE A 74 ILE A 79 -1 O ALA A 76 N TRP A 36
SHEET 5 AA 9 ARG A 45 GLY A 50 1 O ARG A 45 N SER A 75
SHEET 6 AA 9 THR A 138 GLY A 142 1 O GLY A 139 N LEU A 48
SHEET 7 AA 9 ILE A 160 GLY A 166 1 N LYS A 161 O THR A 138
SHEET 8 AA 9 VAL A 189 GLN A 194 1 O ARG A 190 N LEU A 165
SHEET 9 AA 9 LYS A 217 ASN A 222 1 O THR A 218 N TYR A 191
LINK ZN ZN A1248 OE1 GLU A 233 1555 1555 2.15
LINK ZN ZN A1248 OE2 GLU A 233 1555 1555 2.01
LINK ZN ZN A1248 O HOH A2081 1555 1555 2.24
LINK ZN ZN A1248 O HOH A2109 1555 1555 1.97
LINK ZN ZN A1248 ND1 HIS A 220 1555 1555 1.99
LINK ZN ZN A1249 O HOH A2018 1555 1555 2.33
LINK ZN ZN A1249 O HOH A2019 1555 1555 2.00
LINK ZN ZN A1249 NE2 HIS A 51 1555 1555 2.14
LINK ZN ZN A1250 O HOH A2076 1555 4455 2.57
LINK ZN ZN A1250 O HOH A2097 1555 1555 1.76
LINK ZN ZN A1250 OE2 GLU A 198 1555 1555 1.93
CISPEP 1 ASN A 8 GLY A 9 0 0.34
CISPEP 2 GLY A 9 LYS A 10 0 -9.43
CISPEP 3 LYS A 14 LEU A 15 0 19.49
CISPEP 4 GLU A 40 GLY A 41 0 -2.80
SITE 1 AC1 4 HIS A 220 GLU A 233 HOH A2081 HOH A2109
SITE 1 AC2 4 HIS A 51 HOH A2018 HOH A2019 HOH A2022
SITE 1 AC3 5 GLU A 198 HOH A2076 HOH A2095 HOH A2096
SITE 2 AC3 5 HOH A2097
CRYST1 55.660 70.030 53.950 90.00 90.00 90.00 P 21 21 2 4
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 0.017966 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014280 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018536 0.00000
TER 1765 LYS A 247
MASTER 537 0 3 10 9 0 4 6 1890 1 14 20
END |