PDB Short entry for 3NQY HEADER HYDROLASE 30-JUN-10 3NQY TITLE CRYSTAL STRUCTURE OF THE AUTOPROCESSED COMPLEX OF VIBRIOLYSIN MCP-02 TITLE 2 WITH A SINGLE POINT MUTATION E346A COMPND MOL_ID: 1; COMPND 2 MOLECULE: SECRETED METALLOPROTEASE MCP02; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: THE CATALYTIC DOMAIN, RESIDUES 205-519; COMPND 5 SYNONYM: MCP-02; COMPND 6 EC: 3.4.24.25; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SECRETED METALLOPROTEASE MCP02; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: PROPEPTIDE DOMAIN, RESIDUES 25-204; COMPND 13 SYNONYM: MCP-02; COMPND 14 EC: 3.4.24.25; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: PROPEPTIDE OF MCP02 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, PROPEPTIDE, THERMOLYSIN-LIKE PROTEASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.GAO,J.WANG,J.-W.WU,Y.-Z.ZHANG REVDAT 3 02-APR-14 3NQY 1 REMARK VERSN REVDAT 2 27-OCT-10 3NQY 1 JRNL REVDAT 1 06-OCT-10 3NQY 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. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 19341 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 986 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.6795 - 4.9612 0.97 2729 131 0.2010 0.2487 REMARK 3 2 4.9612 - 3.9437 0.99 2615 150 0.1586 0.1765 REMARK 3 3 3.9437 - 3.4469 0.99 2640 121 0.1667 0.2465 REMARK 3 4 3.4469 - 3.1326 1.00 2627 142 0.1873 0.2628 REMARK 3 5 3.1326 - 2.9085 1.00 2572 167 0.2190 0.2870 REMARK 3 6 2.9085 - 2.7372 1.00 2569 140 0.2212 0.3101 REMARK 3 7 2.7372 - 2.6003 1.00 2603 135 0.2272 0.3143 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 31.97 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24260 REMARK 3 B22 (A**2) : 0.24260 REMARK 3 B33 (A**2) : -0.48520 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3755 REMARK 3 ANGLE : 1.195 5093 REMARK 3 CHIRALITY : 0.089 546 REMARK 3 PLANARITY : 0.004 674 REMARK 3 DIHEDRAL : 18.140 1290 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NQY 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 RCSB ID CODE IS RCSB060169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-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 : 19363 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 23.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.67600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: PDB ENTRY 3NQX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 6000, 100MM TRIS BUFFER, PH REMARK 280 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 102.81067 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 51.40533 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 51.40533 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 102.81067 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: 3250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 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 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 SER A 49 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 ASN A 43 CG OD1 ND2 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 ASN B 368 C GLU B 369 N 0.180 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 HIS B 345 O - C - N ANGL. DEV. = -12.6 DEGREES REMARK 500 GLN A 203 O - C - N ANGL. DEV. = -12.7 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 THR B 223 -56.26 -130.85 REMARK 500 SER B 233 96.66 -165.89 REMARK 500 SER B 256 8.83 -153.71 REMARK 500 SER B 276 88.24 -173.00 REMARK 500 SER B 312 -157.02 57.99 REMARK 500 GLU B 316 49.33 -79.84 REMARK 500 SER B 323 -36.19 -130.81 REMARK 500 GLN B 331 -72.82 -149.87 REMARK 500 ASN B 355 -105.72 -125.39 REMARK 500 ASN B 407 73.58 -164.30 REMARK 500 ARG B 413 -29.35 -141.11 REMARK 500 GLN A 41 40.00 -85.79 REMARK 500 SER A 42 82.01 -169.76 REMARK 500 SER A 51 111.31 78.71 REMARK 500 ASP A 93 -175.76 -177.27 REMARK 500 GLU A 117 -77.14 -61.48 REMARK 500 VAL A 122 -9.76 92.56 REMARK 500 ASN A 151 56.01 37.78 REMARK 500 TYR A 177 -132.31 -115.31 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 GLY B 234 ASN B 235 128.71 REMARK 500 SER A 120 ASP A 121 -131.36 REMARK 500 ASP A 121 VAL A 122 108.86 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 A 203 15.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 204 DISTANCE = 5.27 ANGSTROMS REMARK 525 HOH B 529 DISTANCE = 5.28 ANGSTROMS 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 520 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 204 OXT REMARK 620 2 HIS B 345 NE2 117.7 REMARK 620 3 HIS B 349 NE2 102.0 112.3 REMARK 620 4 GLU B 369 OE1 107.6 119.3 94.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 390 O REMARK 620 2 GLU B 380 OE2 154.1 REMARK 620 3 GLU B 377 OE2 78.7 114.2 REMARK 620 4 ASP B 341 OD2 75.8 79.4 101.9 REMARK 620 5 ASP B 388 OD1 78.2 122.2 89.9 148.6 REMARK 620 6 GLU B 380 OE1 157.0 48.8 87.1 125.2 83.9 REMARK 620 7 HOH B 546 O 74.6 95.0 150.8 82.9 73.3 113.9 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 CA B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN 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: 3NQZ RELATED DB: PDB REMARK 900 VIBRIOLYSIN MCP-02 WITH E369A MUTATION DBREF 3NQY B 205 519 UNP A1DRD5 A1DRD5_9GAMM 205 519 DBREF 3NQY A 25 204 UNP A1DRD5 A1DRD5_9GAMM 25 204 SEQADV 3NQY ALA B 346 UNP A1DRD5 GLU 346 ENGINEERED MUTATION 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 ALA 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 GLU 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 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 HET CA B 1 1 HET ZN B 520 1 HETNAM CA CALCIUM ION HETNAM ZN ZINC ION FORMUL 3 CA CA 2+ FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *125(H2 O) HELIX 1 1 SER B 276 GLY B 297 1 22 HELIX 2 2 SER B 339 GLN B 354 1 16 HELIX 3 3 ASN B 361 GLY B 385 1 25 HELIX 4 4 GLY B 392 PHE B 396 5 5 HELIX 5 5 ASN B 407 GLY B 412 5 6 HELIX 6 6 ASN B 417 TYR B 421 5 5 HELIX 7 7 ASP B 426 SER B 431 1 6 HELIX 8 8 SER B 431 THR B 443 1 13 HELIX 9 9 ASP B 448 TYR B 463 1 16 HELIX 10 10 GLY B 469 LEU B 484 1 16 HELIX 11 11 ASP B 487 VAL B 498 1 12 HELIX 12 12 GLN A 33 GLN A 41 1 9 HELIX 13 13 SER A 51 GLY A 57 1 7 HELIX 14 14 ASN A 114 LEU A 119 1 6 HELIX 15 15 THR A 127 SER A 136 1 10 HELIX 16 16 THR A 138 LYS A 143 1 6 SHEET 1 A 2 ASN B 206 ALA B 207 0 SHEET 2 A 2 LEU B 228 ASP B 229 -1 O LEU B 228 N ALA B 207 SHEET 1 B 2 GLY B 209 GLY B 211 0 SHEET 2 B 2 TYR B 219 TYR B 221 -1 O TYR B 221 N GLY B 209 SHEET 1 C 3 SER B 231 GLN B 232 0 SHEET 2 C 3 THR B 236 SER B 238 -1 O SER B 238 N SER B 231 SHEET 3 C 3 SER B 260 THR B 262 -1 O PHE B 261 N CYS B 237 SHEET 1 D 4 VAL B 244 ASN B 248 0 SHEET 2 D 4 LEU B 305 TYR B 311 1 O MET B 307 N ILE B 247 SHEET 3 D 4 MET B 325 GLY B 328 1 O MET B 325 N ARG B 308 SHEET 4 D 4 ALA B 318 TRP B 320 -1 N PHE B 319 O THR B 326 SHEET 1 E 2 LEU B 390 VAL B 391 0 SHEET 2 E 2 ARG B 403 TYR B 404 -1 O ARG B 403 N VAL B 391 SHEET 1 F 5 ASN A 26 TYR A 29 0 SHEET 2 F 5 MET A 103 TYR A 113 -1 O TYR A 113 N ASN A 26 SHEET 3 F 5 VAL A 95 ASN A 100 -1 N SER A 96 O HIS A 108 SHEET 4 F 5 GLU A 76 TYR A 85 -1 N VAL A 77 O PHE A 99 SHEET 5 F 5 ASN A 62 THR A 71 -1 N VAL A 65 O GLN A 82 SHEET 1 G 5 ASN A 26 TYR A 29 0 SHEET 2 G 5 MET A 103 TYR A 113 -1 O TYR A 113 N ASN A 26 SHEET 3 G 5 VAL A 95 ASN A 100 -1 N SER A 96 O HIS A 108 SHEET 4 G 5 GLU A 76 TYR A 85 -1 N VAL A 77 O PHE A 99 SHEET 5 G 5 ILE A 88 PRO A 89 -1 O ILE A 88 N TYR A 85 SHEET 1 H 4 HIS A 150 VAL A 160 0 SHEET 2 H 4 ALA A 166 VAL A 175 -1 O VAL A 175 N HIS A 150 SHEET 3 H 4 PRO A 184 ASP A 189 -1 O ILE A 188 N TYR A 170 SHEET 4 H 4 VAL A 195 ASP A 200 -1 O TYR A 199 N TYR A 185 SSBOND 1 CYS B 237 CYS B 263 1555 1555 1.59 SSBOND 2 CYS B 482 CYS B 510 1555 1555 2.03 LINK OXT HIS A 204 ZN ZN B 520 1555 1555 1.94 LINK NE2 HIS B 345 ZN ZN B 520 1555 1555 1.97 LINK NE2 HIS B 349 ZN ZN B 520 1555 1555 1.97 LINK OE1 GLU B 369 ZN ZN B 520 1555 1555 2.16 LINK O LEU B 390 CA CA B 1 1555 1555 2.43 LINK OE2 GLU B 380 CA CA B 1 1555 1555 2.51 LINK OE2 GLU B 377 CA CA B 1 1555 1555 2.60 LINK OD2 ASP B 341 CA CA B 1 1555 1555 2.62 LINK OD1 ASP B 388 CA CA B 1 1555 1555 2.71 LINK OE1 GLU B 380 CA CA B 1 1555 1555 2.79 LINK CA CA B 1 O HOH B 546 1555 1555 2.42 CISPEP 1 CYS B 263 PRO B 264 0 4.96 CISPEP 2 PHE B 268 LYS B 269 0 0.38 SITE 1 AC1 6 ASP B 341 GLU B 377 GLU B 380 ASP B 388 SITE 2 AC1 6 LEU B 390 HOH B 546 SITE 1 AC2 4 HIS A 204 HIS B 345 HIS B 349 GLU B 369 CRYST1 83.009 83.009 154.216 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 0.012047 0.006955 0.000000 0.00000 SCALE2 0.000000 0.013911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006484 0.00000