HEADER HYDROLASE 30-JUN-10 3NQZ
TITLE CRYSTAL STRUCTURE OF THE AUTOPROCESSED VIBRIOLYSIN MCP-02 WITH E369A
TITLE 2 MUTATION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SECRETED METALLOPROTEASE MCP02;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PROPEPTIDE DOMAIN, RESIDUES 25-204;
COMPND 5 SYNONYM: MCP-02;
COMPND 6 EC: 3.4.24.25;
COMPND 7 ENGINEERED: YES;
COMPND 8 OTHER_DETAILS: PROPEPTIDE OF MCP02;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: SECRETED METALLOPROTEASE MCP02;
COMPND 11 CHAIN: B;
COMPND 12 FRAGMENT: THE CATALYTIC DOMAIN, RESIDUES 205-519;
COMPND 13 SYNONYM: MCP-02;
COMPND 14 EC: 3.4.24.25;
COMPND 15 ENGINEERED: YES;
COMPND 16 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOALTEROMONAS SP.;
SOURCE 3 ORGANISM_TAXID: 234831;
SOURCE 4 STRAIN: SM9913;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B;
SOURCE 10 MOL_ID: 2;
SOURCE 11 ORGANISM_SCIENTIFIC: PSEUDOALTEROMONAS SP.;
SOURCE 12 ORGANISM_TAXID: 234831;
SOURCE 13 STRAIN: SM9913;
SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET21B
KEYWDS AUTOPROCESSED COMPLEX, MCP-02, THE THERMOLYSIN FAMILY, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR X.GAO,J.WANG,L.CHEN,J.-W.WU,Y.-Z.ZHANG
REVDAT 4 01-NOV-23 3NQZ 1 REMARK SEQADV LINK
REVDAT 3 02-APR-14 3NQZ 1 REMARK VERSN
REVDAT 2 27-OCT-10 3NQZ 1 JRNL
REVDAT 1 06-OCT-10 3NQZ 0
JRNL AUTH X.GAO,J.WANG,D.-Q.YU,F.BIAN,B.-B.XIE,X.-L.CHEN,B.-C.ZHOU,
JRNL AUTH 2 L.-H.LAI,Z.-X.WANG,J.-W.WU,Y.-Z.ZHANG
JRNL TITL STRUCTURAL BASIS FOR THE AUTOPROCESSING OF ZINC
JRNL TITL 2 METALLOPROTEASES IN THE THERMOLYSIN FAMILY
JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 17569 2010
JRNL REFN ISSN 0027-8424
JRNL PMID 20876133
JRNL DOI 10.1073/PNAS.1005681107
REMARK 2
REMARK 2 RESOLUTION. 2.05 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.97
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 36839
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) : 0.181
REMARK 3 R VALUE (WORKING SET) : 0.179
REMARK 3 FREE R VALUE : 0.220
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1941
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) : 2.05
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2640
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86
REMARK 3 BIN R VALUE (WORKING SET) : 0.1910
REMARK 3 BIN FREE R VALUE SET COUNT : 160
REMARK 3 BIN FREE R VALUE : 0.2760
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3678
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 2
REMARK 3 SOLVENT ATOMS : 382
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 37.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.20
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.04000
REMARK 3 B22 (A**2) : 0.04000
REMARK 3 B33 (A**2) : -0.06000
REMARK 3 B12 (A**2) : 0.02000
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): 0.166
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.548
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3762 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5105 ; 1.613 ; 1.928
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 479 ; 9.233 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;36.283 ;25.659
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 580 ;15.140 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.227 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 547 ; 0.178 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2931 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1766 ; 0.219 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2576 ; 0.303 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 314 ; 0.145 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.024 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 22 ; 0.203 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.125 ; 0.200
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): 2440 ; 0.890 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3783 ; 1.458 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1547 ; 2.208 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1322 ; 3.043 ; 4.500
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
REMARK 4
REMARK 4 3NQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUL-10.
REMARK 100 THE DEPOSITION ID IS D_1000060170.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-FEB-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
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 FR-E+ DW
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.48
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36839
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050
REMARK 200 RESOLUTION RANGE LOW (A) : 16.970
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 8.600
REMARK 200 R MERGE (I) : 0.07300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 16.50
REMARK 200 R MERGE FOR SHELL (I) : 0.45300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 30.00
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 3NQX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG 10000, TRIS BUFFER, 0.01M NICL2
REMARK 280 , PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
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 102.80400
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 51.40200
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 51.40200
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 102.80400
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: 3310 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19090 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 400
REMARK 400 COMPOUND
REMARK 400 AUTOPROCESSED COMPLEX
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 SER A 44
REMARK 465 ALA A 45
REMARK 465 SER A 46
REMARK 465 LEU A 47
REMARK 465 LEU A 48
REMARK 465 THR B 512
REMARK 465 PRO B 513
REMARK 465 GLN B 514
REMARK 465 PRO B 515
REMARK 465 PRO B 516
REMARK 465 THR B 517
REMARK 465 ASP B 518
REMARK 465 ASP B 519
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 LEU A 119 CG CD1 CD2
REMARK 470 SER A 120 OG
REMARK 470 ASP A 121 CG OD1 OD2
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 CYS B 237 CB CYS B 237 SG -0.110
REMARK 500 GLU B 346 CD GLU B 346 OE1 -0.066
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 SER A 59 O - C - N ANGL. DEV. = 11.6 DEGREES
REMARK 500 ASP A 121 O - C - N ANGL. DEV. = 14.5 DEGREES
REMARK 500 VAL A 122 C - N - CA ANGL. DEV. = 16.5 DEGREES
REMARK 500 GLY B 234 N - CA - C ANGL. DEV. = -17.2 DEGREES
REMARK 500 ASN B 266 N - CA - C ANGL. DEV. = 19.9 DEGREES
REMARK 500 ASP B 341 CB - CG - OD1 ANGL. DEV. = 6.3 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 SER A 42 59.20 150.34
REMARK 500 VAL A 122 22.54 -70.36
REMARK 500 ASN A 164 19.07 59.35
REMARK 500 TYR A 177 -128.26 -107.60
REMARK 500 THR B 223 -65.90 -123.84
REMARK 500 ASN B 235 50.60 -102.99
REMARK 500 SER B 256 16.38 -142.41
REMARK 500 SER B 276 87.79 -169.56
REMARK 500 SER B 312 -155.29 62.20
REMARK 500 SER B 323 -36.27 -134.25
REMARK 500 GLN B 331 -66.57 -156.10
REMARK 500 LEU B 337 21.52 -76.90
REMARK 500 GLU B 346 -66.53 92.00
REMARK 500 ASN B 355 -100.44 -122.41
REMARK 500 ASN B 361 143.34 -172.22
REMARK 500 ASN B 407 69.19 -159.27
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 ASP A 121 VAL A 122 130.00
REMARK 500 SER B 233 GLY B 234 -112.08
REMARK 500 GLU B 265 ASN B 266 131.02
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 GLN B 306 -11.08
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 B 1 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 204 OXT
REMARK 620 2 HIS B 345 NE2 117.9
REMARK 620 3 HIS B 349 NE2 90.6 104.4
REMARK 620 4 HIS B 428 NE2 96.4 117.3 127.4
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 520 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 341 OD2
REMARK 620 2 GLU B 377 OE2 96.7
REMARK 620 3 GLU B 380 OE2 73.9 111.9
REMARK 620 4 GLU B 380 OE1 120.8 88.8 50.1
REMARK 620 5 ASP B 388 OD1 153.1 102.8 114.5 78.4
REMARK 620 6 LEU B 390 O 77.9 96.4 141.8 160.1 81.7
REMARK 620 7 HOH B 638 O 80.9 168.9 78.0 101.8 76.4 72.6
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 ZN B 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 520
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3NQX RELATED DB: PDB
REMARK 900 VIBRIOLYSIN MCP-02
REMARK 900 RELATED ID: 3NQY RELATED DB: PDB
REMARK 900 VIBRIOLYSIN MCP-02 WITH A SINGLE POINT MUTATION E346A
DBREF 3NQZ A 25 204 UNP A1DRD5 A1DRD5_9GAMM 25 204
DBREF 3NQZ B 205 519 UNP A1DRD5 A1DRD5_9GAMM 205 519
SEQADV 3NQZ ALA B 369 UNP A1DRD5 GLU 369 ENGINEERED MUTATION
SEQRES 1 A 180 ALA ASN LYS LYS TYR LEU ASN GLN GLN PRO THR ILE ASN
SEQRES 2 A 180 ASN MET VAL GLN SER ASN SER ALA SER LEU LEU SER VAL
SEQRES 3 A 180 SER PRO ASN GLN LEU ILE GLY LEU SER VAL GLY ASN GLU
SEQRES 4 A 180 LEU VAL VAL LEU LYS GLU PHE THR SER ASN ASN GLY GLU
SEQRES 5 A 180 VAL THR ARG ARG TYR GLN GLN THR TYR GLN GLY ILE PRO
SEQRES 6 A 180 VAL ILE GLY ASP THR VAL SER LEU THR PHE ASN ASN GLY
SEQRES 7 A 180 MET LEU LYS LYS ALA HIS GLY ALA ALA VAL TYR ASN ILE
SEQRES 8 A 180 ASP GLU ASP LEU SER ASP VAL SER ALA LYS LEU THR LYS
SEQRES 9 A 180 LYS ASP ALA ILE LEU LYS GLY SER LYS THR GLY ILE ALA
SEQRES 10 A 180 ALA LYS SER VAL GLY LEU LYS LYS HIS ASN GLU GLN SER
SEQRES 11 A 180 ARG LEU ALA ILE TRP VAL ASP ASP GLN ASN LYS ALA HIS
SEQRES 12 A 180 LEU VAL TYR GLU VAL SER TYR VAL THR TYR GLY LYS SER
SEQRES 13 A 180 PRO SER ARG PRO TYR LEU ILE ILE ASP ALA ASN THR GLY
SEQRES 14 A 180 GLU VAL LEU LEU SER TYR ASP ASN LEU GLN HIS
SEQRES 1 B 315 ALA ASN ALA THR GLY PRO GLY GLY ASN LEU LYS THR GLY
SEQRES 2 B 315 LYS TYR LEU TYR GLY THR ASP PHE ASP SER LEU ASP VAL
SEQRES 3 B 315 SER GLN SER GLY ASN THR CYS SER MET ASN ASN ALA ASN
SEQRES 4 B 315 VAL ARG THR ILE ASN LEU ASN GLY GLY THR SER GLY SER
SEQRES 5 B 315 SER ALA TYR SER PHE THR CYS PRO GLU ASN THR PHE LYS
SEQRES 6 B 315 GLU ILE ASN GLY ALA TYR SER PRO LEU ASN ASP ALA HIS
SEQRES 7 B 315 PHE PHE GLY ASN VAL ILE PHE ASN MET TYR ASN ASP TRP
SEQRES 8 B 315 LEU GLY THR ALA PRO LEU SER PHE GLN LEU GLN MET ARG
SEQRES 9 B 315 VAL HIS TYR SER SER ASN TYR GLU ASN ALA PHE TRP ASP
SEQRES 10 B 315 GLY SER ALA MET THR PHE GLY ASP GLY GLN ASN THR PHE
SEQRES 11 B 315 TYR PRO LEU VAL SER LEU ASP VAL SER ALA HIS GLU VAL
SEQRES 12 B 315 SER HIS GLY PHE THR GLU GLN ASN SER GLY LEU ILE TYR
SEQRES 13 B 315 ASN GLY LYS PRO GLY GLY LEU ASN ALA ALA PHE SER ASP
SEQRES 14 B 315 MET ALA GLY GLU ALA ALA GLU PHE TYR MET LYS GLY SER
SEQRES 15 B 315 ASN ASP TRP LEU VAL GLY LYS ASP ILE PHE LYS GLY ASN
SEQRES 16 B 315 GLY ALA LEU ARG TYR MET ASN ASN PRO THR GLN ASP GLY
SEQRES 17 B 315 ARG SER ILE ASP ASN GLN SER ASN TYR TYR SER GLY MET
SEQRES 18 B 315 ASP VAL HIS TYR SER SER GLY VAL TYR ASN LYS ALA PHE
SEQRES 19 B 315 TYR ASN LEU ALA THR THR PRO GLY TRP ASP THR GLN LYS
SEQRES 20 B 315 ALA PHE ILE VAL MET ALA ARG ALA ASN GLN LEU TYR TRP
SEQRES 21 B 315 SER ALA GLY VAL GLY TRP ASP LEU ALA GLY ASN GLY VAL
SEQRES 22 B 315 MET ASP ALA ALA CYS ASP LEU ASN TYR ASP PRO ASN ASP
SEQRES 23 B 315 VAL LYS ALA ALA LEU ALA ALA VAL GLY VAL ASN SER ASN
SEQRES 24 B 315 LEU SER SER GLY SER ASP CYS ALA THR PRO GLN PRO PRO
SEQRES 25 B 315 THR ASP ASP
HET ZN B 1 1
HET CA B 520 1
HETNAM ZN ZINC ION
HETNAM CA CALCIUM ION
FORMUL 3 ZN ZN 2+
FORMUL 4 CA CA 2+
FORMUL 5 HOH *382(H2 O)
HELIX 1 1 GLN A 33 GLN A 41 1 9
HELIX 2 2 SER A 51 GLY A 57 1 7
HELIX 3 3 ASN A 114 ASP A 118 5 5
HELIX 4 4 THR A 127 SER A 136 1 10
HELIX 5 5 THR A 138 VAL A 145 1 8
HELIX 6 6 SER B 276 GLY B 297 1 22
HELIX 7 7 SER B 339 ASN B 355 1 17
HELIX 8 8 ASN B 361 GLY B 385 1 25
HELIX 9 9 GLY B 392 PHE B 396 5 5
HELIX 10 10 ASN B 407 GLY B 412 5 6
HELIX 11 11 ASN B 417 TYR B 421 5 5
HELIX 12 12 ASP B 426 SER B 431 1 6
HELIX 13 13 SER B 431 THR B 443 1 13
HELIX 14 14 ASP B 448 TYR B 463 1 16
HELIX 15 15 GLY B 469 LEU B 484 1 16
HELIX 16 16 ASP B 487 ALA B 497 1 11
SHEET 1 A 5 ASN A 26 TYR A 29 0
SHEET 2 A 5 MET A 103 TYR A 113 -1 O TYR A 113 N ASN A 26
SHEET 3 A 5 VAL A 95 ASN A 100 -1 N SER A 96 O HIS A 108
SHEET 4 A 5 GLU A 76 TYR A 85 -1 N ARG A 79 O LEU A 97
SHEET 5 A 5 ASN A 62 THR A 71 -1 N LEU A 67 O ARG A 80
SHEET 1 B 5 ASN A 26 TYR A 29 0
SHEET 2 B 5 MET A 103 TYR A 113 -1 O TYR A 113 N ASN A 26
SHEET 3 B 5 VAL A 95 ASN A 100 -1 N SER A 96 O HIS A 108
SHEET 4 B 5 GLU A 76 TYR A 85 -1 N ARG A 79 O LEU A 97
SHEET 5 B 5 ILE A 88 PRO A 89 -1 O ILE A 88 N TYR A 85
SHEET 1 C 4 HIS A 150 VAL A 160 0
SHEET 2 C 4 ALA A 166 VAL A 175 -1 O SER A 173 N GLN A 153
SHEET 3 C 4 PRO A 184 ASP A 189 -1 O ILE A 188 N TYR A 170
SHEET 4 C 4 VAL A 195 ASP A 200 -1 O LEU A 196 N ILE A 187
SHEET 1 D 2 ASN B 206 ALA B 207 0
SHEET 2 D 2 LEU B 228 ASP B 229 -1 O LEU B 228 N ALA B 207
SHEET 1 E 2 GLY B 209 ASN B 213 0
SHEET 2 E 2 GLY B 217 TYR B 221 -1 O TYR B 221 N GLY B 209
SHEET 1 F 3 SER B 231 SER B 233 0
SHEET 2 F 3 THR B 236 SER B 238 -1 O SER B 238 N SER B 231
SHEET 3 F 3 SER B 260 THR B 262 -1 O PHE B 261 N CYS B 237
SHEET 1 G 4 VAL B 244 ASN B 248 0
SHEET 2 G 4 LEU B 305 TYR B 311 1 O MET B 307 N ILE B 247
SHEET 3 G 4 MET B 325 GLY B 328 1 O MET B 325 N ARG B 308
SHEET 4 G 4 ALA B 318 TRP B 320 -1 N PHE B 319 O THR B 326
SSBOND 1 CYS B 237 CYS B 263 1555 1555 2.10
SSBOND 2 CYS B 482 CYS B 510 1555 1555 2.06
LINK OXT HIS A 204 ZN ZN B 1 1555 1555 1.84
LINK ZN ZN B 1 NE2 HIS B 345 1555 1555 1.94
LINK ZN ZN B 1 NE2 HIS B 349 1555 1555 2.10
LINK ZN ZN B 1 NE2 HIS B 428 1555 1555 2.03
LINK OD2 ASP B 341 CA CA B 520 1555 1555 2.57
LINK OE2 GLU B 377 CA CA B 520 1555 1555 2.49
LINK OE2 GLU B 380 CA CA B 520 1555 1555 2.46
LINK OE1 GLU B 380 CA CA B 520 1555 1555 2.73
LINK OD1 ASP B 388 CA CA B 520 1555 1555 2.51
LINK O LEU B 390 CA CA B 520 1555 1555 2.41
LINK CA CA B 520 O HOH B 638 1555 1555 2.51
CISPEP 1 GLY B 234 ASN B 235 0 -7.73
CISPEP 2 CYS B 263 PRO B 264 0 -1.36
CISPEP 3 PHE B 268 LYS B 269 0 -7.42
SITE 1 AC1 4 HIS A 204 HIS B 345 HIS B 349 HIS B 428
SITE 1 AC2 6 ASP B 341 GLU B 377 GLU B 380 ASP B 388
SITE 2 AC2 6 LEU B 390 HOH B 638
CRYST1 82.535 82.535 154.206 90.00 90.00 120.00 P 32 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 0.012116 0.006995 0.000000 0.00000
SCALE2 0.000000 0.013990 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006485 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
