HEADER HYDROLASE 10-NOV-09 2WXT TITLE CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN STRAIN NCTC8237 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PLC, PHOSPHATIDYLCHOLINE CHOLINEPHOSPHOHYDROLASE, ALPHA- COMPND 5 TOXIN, HEMOLYSIN, LECITHINASE; COMPND 6 EC: 3.1.4.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 3 ORGANISM_TAXID: 1502; SOURCE 4 STRAIN: NCTC8237; SOURCE 5 ATCC: 19408; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: JM109; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKSA3 KEYWDS CYTOLYSIS, HYDROLASE, HEMOLYSIS, MEMBRANE BINDING, GANGRENE KEYWDS 2 DETERMINANT, C2 DOMAIN, VIRULENCE EXPDTA X-RAY DIFFRACTION AUTHOR N.JUSTIN,C.E.NAYLOR,A.K.BASAK REVDAT 5 20-DEC-23 2WXT 1 REMARK LINK REVDAT 4 10-APR-19 2WXT 1 SOURCE REVDAT 3 27-OCT-10 2WXT 1 JRNL REVDAT 2 29-SEP-10 2WXT 1 KEYWDS JRNL REMARK MASTER REVDAT 1 17-NOV-09 2WXT 0 JRNL AUTH S.G.VACHIERI,G.C.CLARK,A.ALAPE-GIRON,M.FLORES-DIAZ,N.JUSTIN, JRNL AUTH 2 C.E.NAYLOR,R.W.TITBALL,A.K.BASAK JRNL TITL COMPARISON OF A NONTOXIC VARIANT OF CLOSTRIDIUM PERFRINGENS JRNL TITL 2 [ALPHA]-TOXIN WITH THE TOXIC WILD-TYPE STRAIN JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 66 1067 2010 JRNL REFN ISSN 0907-4449 JRNL PMID 20944240 JRNL DOI 10.1107/S090744491003369X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.E.NAYLOR,J.T.EATON,A.HOWELLS,N.JUSTIN,D.S.MOSS, REMARK 1 AUTH 2 R.W.TITBALL,A.K.BASAK REMARK 1 TITL STRUCTURE OF THE KEY TOXIN IN GAS GANGRENE. REMARK 1 REF NAT.STRUCT.BIOL. V. 5 738 1998 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 9699639 REMARK 1 DOI 10.1038/1447 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 25554 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1378 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 29.0647 - 4.3047 0.82 2357 142 0.1927 0.2265 REMARK 3 2 4.3047 - 3.4185 0.87 2414 113 0.1551 0.2059 REMARK 3 3 3.4185 - 2.9869 0.88 2392 151 0.1638 0.2370 REMARK 3 4 2.9869 - 2.7140 0.89 2427 122 0.1700 0.2286 REMARK 3 5 2.7140 - 2.5196 0.90 2434 139 0.1673 0.2437 REMARK 3 6 2.5196 - 2.3711 0.90 2411 143 0.1639 0.2523 REMARK 3 7 2.3711 - 2.2524 0.90 2433 132 0.1656 0.2132 REMARK 3 8 2.2524 - 2.1544 0.91 2403 160 0.1690 0.2274 REMARK 3 9 2.1544 - 2.0715 0.91 2460 137 0.1877 0.2672 REMARK 3 10 2.0715 - 2.0000 0.92 2445 139 0.2159 0.2635 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 : 0.43 REMARK 3 B_SOL : 61.25 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.55080 REMARK 3 B22 (A**2) : -4.79140 REMARK 3 B33 (A**2) : -2.75940 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 : 0.014 2973 REMARK 3 ANGLE : 1.346 4021 REMARK 3 CHIRALITY : 0.089 411 REMARK 3 PLANARITY : 0.006 521 REMARK 3 DIHEDRAL : 17.427 1052 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 1:244 REMARK 3 ORIGIN FOR THE GROUP (A): 15.9331 69.0498 38.1608 REMARK 3 T TENSOR REMARK 3 T11: 0.0744 T22: 0.0784 REMARK 3 T33: 0.0937 T12: 0.0485 REMARK 3 T13: -0.0179 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.8452 L22: 2.2034 REMARK 3 L33: 1.6726 L12: -0.0425 REMARK 3 L13: -0.2247 L23: -0.3375 REMARK 3 S TENSOR REMARK 3 S11: 0.0480 S12: 0.0232 S13: -0.0244 REMARK 3 S21: -0.0880 S22: -0.0762 S23: 0.0604 REMARK 3 S31: -0.1345 S32: -0.0491 S33: 0.0288 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 245:370 REMARK 3 ORIGIN FOR THE GROUP (A): -5.6520 51.3493 36.9425 REMARK 3 T TENSOR REMARK 3 T11: 0.0492 T22: 0.2508 REMARK 3 T33: 0.2303 T12: -0.0024 REMARK 3 T13: 0.0353 T23: 0.0329 REMARK 3 L TENSOR REMARK 3 L11: 1.5118 L22: 1.5271 REMARK 3 L33: 0.8511 L12: 0.5527 REMARK 3 L13: 0.4868 L23: -0.0404 REMARK 3 S TENSOR REMARK 3 S11: 0.0702 S12: -0.1967 S13: 0.1432 REMARK 3 S21: 0.0170 S22: 0.0136 S23: 0.0442 REMARK 3 S31: -0.0035 S32: -0.1271 S33: -0.0607 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 2WXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1290041677. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SILICON (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25562 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1CA1 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M NA ACETATE, 0.1 M NA-HEPES, PH7.6, REMARK 280 0.05 M CDSO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 39.76500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.76500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 30.09000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 87.18500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.09000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 87.18500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.76500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.09000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 87.18500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.76500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.09000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 87.18500 REMARK 290 SMTRY3 8 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 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 ASN A 76 REMARK 465 ASN A 77 REMARK 465 PHE A 78 REMARK 465 SER A 79 REMARK 465 LYS A 80 REMARK 465 ASP A 81 REMARK 465 ASN A 82 REMARK 465 SER A 83 REMARK 465 TRP A 84 REMARK 465 TYR A 85 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 29 CG OD1 ND2 REMARK 470 ASP A 63 CG OD1 OD2 REMARK 470 ASP A 75 CA C O CB CG OD1 OD2 REMARK 470 LYS A 330 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASP A 336 O SER A 362 2.11 REMARK 500 O HOH A 2108 O HOH A 2109 2.13 REMARK 500 O HOH A 2038 O HOH A 2040 2.18 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 TRP A 70 119.98 -170.51 REMARK 500 HIS A 207 -33.20 -146.96 REMARK 500 ASP A 336 -176.43 -60.86 REMARK 500 ILE A 357 -71.20 -112.61 REMARK 500 ASN A 364 44.61 -101.01 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 A1371 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 1 O REMARK 620 2 TRP A 1 N 72.1 REMARK 620 3 HIS A 11 NE2 94.0 109.3 REMARK 620 4 ASP A 130 OD2 168.5 96.7 92.4 REMARK 620 5 HOH A2243 O 93.3 130.6 118.8 92.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1372 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 46 ND1 REMARK 620 2 GLU A 47 OE2 122.9 REMARK 620 3 GLU A 359 OE1 59.7 131.3 REMARK 620 4 GLU A 359 OE2 99.9 84.2 51.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1373 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 56 OD1 REMARK 620 2 HIS A 68 ND1 92.1 REMARK 620 3 HIS A 126 NE2 85.6 91.8 REMARK 620 4 ASP A 130 OD1 177.3 90.5 93.5 REMARK 620 5 HOH A2065 O 86.6 88.8 172.3 94.2 REMARK 620 6 HOH A2243 O 80.2 165.8 99.4 97.5 78.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1374 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 136 NE2 REMARK 620 2 HIS A 148 NE2 91.0 REMARK 620 3 GLU A 152 OE1 142.3 89.0 REMARK 620 4 GLU A 152 OE2 91.8 97.2 50.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1375 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 157 OE1 REMARK 620 2 GLU A 157 OE1 65.1 REMARK 620 3 GLU A 157 OE2 109.8 50.4 REMARK 620 4 GLU A 157 OE2 53.0 118.0 149.7 REMARK 620 5 HOH A2118 O 154.0 140.9 94.5 101.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1376 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 168 O REMARK 620 2 CYS A 169 SG 79.6 REMARK 620 3 HIS A 207 NE2 177.3 99.0 REMARK 620 4 HOH A2124 O 75.2 113.7 103.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1377 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 169 SG REMARK 620 2 GLU A 173 OE2 84.8 REMARK 620 3 GLU A 173 OE1 76.0 56.2 REMARK 620 4 ASP A 216 OD1 101.6 94.4 150.5 REMARK 620 5 HOH A2125 O 100.5 142.1 88.4 120.5 REMARK 620 6 HOH A2160 O 164.2 79.7 92.7 82.7 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1378 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 173 OE2 REMARK 620 2 HIS A 212 ND1 166.6 REMARK 620 3 ASP A 216 OD2 83.2 105.0 REMARK 620 4 HOH A2154 O 76.3 91.6 99.8 REMARK 620 5 HOH A2159 O 101.1 73.9 164.2 96.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1379 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 241 ND1 REMARK 620 2 GLU A 245 OE2 93.7 REMARK 620 3 GLU A 245 OE1 108.0 54.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1380 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 273 OD2 REMARK 620 2 ASP A 273 OD1 121.8 REMARK 620 3 ASP A 273 OD1 53.2 119.6 REMARK 620 4 ASN A 297 OD1 108.7 127.2 101.7 REMARK 620 5 HOH A2190 O 112.3 53.9 160.8 95.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1381 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 293 OD2 REMARK 620 2 ASP A 293 OD1 49.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1373 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1374 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1375 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1376 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1377 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1378 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1379 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1380 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1381 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QM6 RELATED DB: PDB REMARK 900 CLOSED FORM OF C. PERFRINGENS ALPHA-TOXIN STRAIN NCTC8237 REMARK 900 RELATED ID: 1QMD RELATED DB: PDB REMARK 900 CALCIUM BOUND CLOSED FORM ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS REMARK 900 RELATED ID: 2WXU RELATED DB: PDB REMARK 900 CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN STRAIN NCTC8237 MUTANT T74I REMARK 900 RELATED ID: 2WY6 RELATED DB: PDB REMARK 900 CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN STRAIN NCTC8237 MUTANT T74I DBREF 2WXT A 1 370 UNP Q0TV31 PHLC_CLOP1 29 398 SEQRES 1 A 370 TRP ASP GLY LYS ILE ASP GLY THR GLY THR HIS ALA MET SEQRES 2 A 370 ILE VAL THR GLN GLY VAL SER ILE LEU GLU ASN ASP LEU SEQRES 3 A 370 SER LYS ASN GLU PRO GLU SER VAL ARG LYS ASN LEU GLU SEQRES 4 A 370 ILE LEU LYS GLU ASN MET HIS GLU LEU GLN LEU GLY SER SEQRES 5 A 370 THR TYR PRO ASP TYR ASP LYS ASN ALA TYR ASP LEU TYR SEQRES 6 A 370 GLN ASP HIS PHE TRP ASP PRO ASP THR ASP ASN ASN PHE SEQRES 7 A 370 SER LYS ASP ASN SER TRP TYR LEU ALA TYR SER ILE PRO SEQRES 8 A 370 ASP THR GLY GLU SER GLN ILE ARG LYS PHE SER ALA LEU SEQRES 9 A 370 ALA ARG TYR GLU TRP GLN ARG GLY ASN TYR LYS GLN ALA SEQRES 10 A 370 THR PHE TYR LEU GLY GLU ALA MET HIS TYR PHE GLY ASP SEQRES 11 A 370 ILE ASP THR PRO TYR HIS PRO ALA ASN VAL THR ALA VAL SEQRES 12 A 370 ASP SER ALA GLY HIS VAL LYS PHE GLU THR PHE ALA GLU SEQRES 13 A 370 GLU ARG LYS GLU GLN TYR LYS ILE ASN THR ALA GLY CYS SEQRES 14 A 370 LYS THR ASN GLU ALA PHE TYR THR ASP ILE LEU LYS ASN SEQRES 15 A 370 LYS ASP PHE ASN ALA TRP SER LYS GLU TYR ALA ARG GLY SEQRES 16 A 370 PHE ALA LYS THR GLY LYS SER ILE TYR TYR SER HIS ALA SEQRES 17 A 370 SER MET SER HIS SER TRP ASP ASP TRP ASP TYR ALA ALA SEQRES 18 A 370 LYS VAL THR LEU ALA ASN SER GLN LYS GLY THR ALA GLY SEQRES 19 A 370 TYR ILE TYR ARG PHE LEU HIS ASP VAL SER GLU GLY ASN SEQRES 20 A 370 ASP PRO SER VAL GLY LYS ASN VAL LYS GLU LEU VAL ALA SEQRES 21 A 370 TYR ILE SER THR SER GLY GLU LYS ASP ALA GLY THR ASP SEQRES 22 A 370 ASP TYR MET TYR PHE GLY ILE LYS THR LYS ASP GLY LYS SEQRES 23 A 370 THR GLN GLU TRP GLU MET ASP ASN PRO GLY ASN ASP PHE SEQRES 24 A 370 MET THR GLY SER LYS ASP THR TYR THR PHE LYS LEU LYS SEQRES 25 A 370 ASP GLU ASN LEU LYS ILE ASP ASP ILE GLN ASN MET TRP SEQRES 26 A 370 ILE ARG LYS ARG LYS TYR THR ALA PHE SER ASP ALA TYR SEQRES 27 A 370 LYS PRO GLU ASN ILE LYS ILE ILE ALA ASN GLY LYS VAL SEQRES 28 A 370 VAL VAL ASP LYS ASP ILE ASN GLU TRP ILE SER GLY ASN SEQRES 29 A 370 SER THR TYR ASN ILE LYS HET ZN A1371 1 HET CD A1372 1 HET CD A1373 1 HET CD A1374 1 HET CD A1375 1 HET CD A1376 1 HET CD A1377 1 HET CD A1378 1 HET CD A1379 1 HET CA A1380 1 HET CA A1381 1 HETNAM ZN ZINC ION HETNAM CD CADMIUM ION HETNAM CA CALCIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 CD 8(CD 2+) FORMUL 11 CA 2(CA 2+) FORMUL 13 HOH *243(H2 O) HELIX 1 1 GLY A 9 LEU A 26 1 18 HELIX 2 2 PRO A 31 ASN A 44 1 14 HELIX 3 3 ASN A 44 TYR A 54 1 11 HELIX 4 4 PRO A 55 TYR A 57 5 3 HELIX 5 5 TYR A 65 PHE A 69 5 5 HELIX 6 6 THR A 93 ARG A 111 1 19 HELIX 7 7 ASN A 113 ASP A 132 1 20 HELIX 8 8 ALA A 146 ARG A 158 1 13 HELIX 9 9 LYS A 159 LYS A 163 5 5 HELIX 10 10 GLU A 173 ASN A 182 1 10 HELIX 11 11 ASP A 184 HIS A 207 1 24 HELIX 12 12 SER A 213 GLY A 246 1 34 HELIX 13 13 LYS A 317 ASP A 319 5 3 SHEET 1 AA 4 LYS A 304 LYS A 310 0 SHEET 2 AA 4 GLU A 257 THR A 264 -1 O LEU A 258 N PHE A 309 SHEET 3 AA 4 PRO A 340 ALA A 347 -1 N GLU A 341 O SER A 263 SHEET 4 AA 4 LYS A 350 ASP A 356 -1 O LYS A 350 N ALA A 347 SHEET 1 AB 4 THR A 287 GLU A 291 0 SHEET 2 AB 4 TYR A 275 THR A 282 -1 O PHE A 278 N TRP A 290 SHEET 3 AB 4 ILE A 321 ARG A 329 -1 N GLN A 322 O LYS A 281 SHEET 4 AB 4 THR A 366 ASN A 368 -1 O TYR A 367 N ILE A 326 LINK O TRP A 1 ZN ZN A1371 1555 1555 2.30 LINK N TRP A 1 ZN ZN A1371 1555 1555 2.21 LINK NE2 HIS A 11 ZN ZN A1371 1555 1555 2.07 LINK ND1 HIS A 46 CD CD A1372 1555 1555 2.37 LINK OE2 GLU A 47 CD CD A1372 1555 1555 2.39 LINK OD1 ASP A 56 CD CD A1373 1555 1555 2.46 LINK ND1 HIS A 68 CD CD A1373 1555 1555 2.16 LINK NE2 HIS A 126 CD CD A1373 1555 1555 2.43 LINK OD2 ASP A 130 ZN ZN A1371 1555 1555 2.17 LINK OD1 ASP A 130 CD CD A1373 1555 1555 2.38 LINK NE2 HIS A 136 CD CD A1374 1555 1555 2.31 LINK NE2 HIS A 148 CD CD A1374 1555 1555 2.46 LINK OE1 GLU A 152 CD CD A1374 1555 1555 2.18 LINK OE2 GLU A 152 CD CD A1374 1555 1555 2.71 LINK OE1 GLU A 157 CD CD A1375 1555 1555 2.43 LINK OE1 GLU A 157 CD CD A1375 3655 1555 2.41 LINK OE2 GLU A 157 CD CD A1375 3655 1555 2.72 LINK OE2 GLU A 157 CD CD A1375 1555 1555 2.51 LINK O GLY A 168 CD CD A1376 1555 1555 2.74 LINK SG CYS A 169 CD CD A1376 1555 1555 2.58 LINK SG CYS A 169 CD CD A1377 1555 1555 2.89 LINK OE2 GLU A 173 CD CD A1377 1555 1555 2.28 LINK OE1 GLU A 173 CD CD A1377 1555 1555 2.45 LINK OE2 GLU A 173 CD CD A1378 1555 1555 2.21 LINK NE2 HIS A 207 CD CD A1376 4566 1555 2.43 LINK ND1 HIS A 212 CD CD A1378 4566 1555 2.39 LINK OD1 ASP A 216 CD CD A1377 4566 1555 2.36 LINK OD2 ASP A 216 CD CD A1378 4566 1555 2.38 LINK ND1 HIS A 241 CD CD A1379 1555 1555 2.43 LINK OE2 GLU A 245 CD CD A1379 1555 1555 2.40 LINK OE1 GLU A 245 CD CD A1379 1555 1555 2.35 LINK OD2 ASP A 273 CA CA A1380 3555 1555 2.54 LINK OD1 ASP A 273 CA CA A1380 1555 1555 2.78 LINK OD1 ASP A 273 CA CA A1380 3555 1555 2.50 LINK OD2 ASP A 293 CA CA A1381 1555 1555 2.78 LINK OD1 ASP A 293 CA CA A1381 1555 1555 2.50 LINK OD1 ASN A 297 CA CA A1380 1555 1555 2.16 LINK OE1 GLU A 359 CD CD A1372 8556 1555 2.71 LINK OE2 GLU A 359 CD CD A1372 8556 1555 2.48 LINK ZN ZN A1371 O HOH A2243 1555 1555 2.18 LINK CD CD A1373 O HOH A2065 1555 1555 2.52 LINK CD CD A1373 O HOH A2243 1555 1555 1.95 LINK CD CD A1375 O HOH A2118 1555 3655 2.21 LINK CD CD A1376 O HOH A2124 1555 1555 2.72 LINK CD CD A1377 O HOH A2125 1555 1555 2.79 LINK CD CD A1377 O HOH A2160 1555 4566 2.48 LINK CD CD A1378 O HOH A2154 1555 4566 2.58 LINK CD CD A1378 O HOH A2159 1555 4566 2.65 LINK CA CA A1380 O HOH A2190 1555 1555 2.44 SITE 1 AC1 5 TRP A 1 HIS A 11 ASP A 130 CD A1373 SITE 2 AC1 5 HOH A2243 SITE 1 AC2 3 HIS A 46 GLU A 47 GLU A 359 SITE 1 AC3 7 ASP A 56 HIS A 68 HIS A 126 ASP A 130 SITE 2 AC3 7 ZN A1371 HOH A2065 HOH A2243 SITE 1 AC4 3 HIS A 136 HIS A 148 GLU A 152 SITE 1 AC5 2 GLU A 157 HOH A2118 SITE 1 AC6 5 GLY A 168 CYS A 169 HIS A 207 HOH A2124 SITE 2 AC6 5 HOH A2156 SITE 1 AC7 5 CYS A 169 GLU A 173 ASP A 216 HOH A2125 SITE 2 AC7 5 HOH A2160 SITE 1 AC8 5 GLU A 173 HIS A 212 ASP A 216 HOH A2154 SITE 2 AC8 5 HOH A2159 SITE 1 AC9 2 HIS A 241 GLU A 245 SITE 1 BC1 3 ASP A 273 ASN A 297 HOH A2190 SITE 1 BC2 1 ASP A 293 CRYST1 60.180 174.370 79.530 90.00 90.00 90.00 C 2 2 21 8 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 0.016617 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005735 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012574 0.00000