HEADER TOXIN 30-NOV-01 1KHO TITLE CRYSTAL STRUCTURE ANALYSIS OF CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN TITLE 2 ISOLATED FROM AVIAN STRAIN SWCP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-TOXIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 3 ORGANISM_TAXID: 1502; SOURCE 4 GENE: CPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS N-TERMINAL ALPHA-HELIX, C-TERMINAL BETA-SHEET, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR N.JUSTIN,D.S.MOSS,R.W.TITBALL,A.K.BASAK REVDAT 3 14-FEB-24 1KHO 1 REMARK LINK REVDAT 2 24-FEB-09 1KHO 1 VERSN REVDAT 1 19-JUN-02 1KHO 0 JRNL AUTH N.JUSTIN,N.WALKER,H.L.BULLIFENT,G.SONGER,D.M.BUESCHEL, JRNL AUTH 2 H.JOST,C.NAYLOR,J.MILLER,D.S.MOSS,R.W.TITBALL,A.K.BASAK JRNL TITL THE FIRST STRAIN OF CLOSTRIDIUM PERFRINGENS ISOLATED FROM AN JRNL TITL 2 AVIAN SOURCE HAS AN ALPHA-TOXIN WITH DIVERGENT STRUCTURAL JRNL TITL 3 AND KINETIC PROPERTIES. JRNL REF BIOCHEMISTRY V. 41 6253 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12009886 JRNL DOI 10.1021/BI012015V REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 59406 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4828 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5990 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.490 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000014972. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 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) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.18700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA ACETATE, ACETONE, NA CACODYLATE, PH REMARK 280 6.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 110.29500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.14750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 165.44250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 110.29500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 165.44250 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.14750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ARG B 194 NE - CZ - NH2 ANGL. DEV. = -3.3 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 44 30.20 -99.29 REMARK 500 ASN A 60 -155.33 -116.96 REMARK 500 ASP A 75 22.45 -43.98 REMARK 500 ASN A 76 75.07 161.60 REMARK 500 ASP A 248 15.73 -68.89 REMARK 500 SER A 249 7.74 45.87 REMARK 500 SER A 250 127.40 67.41 REMARK 500 ILE A 357 -70.73 -119.63 REMARK 500 ASN B 60 -151.79 -147.03 REMARK 500 ASP B 75 -11.26 -47.79 REMARK 500 PHE B 78 87.59 38.25 REMARK 500 ASP B 81 127.08 -29.54 REMARK 500 ASP B 248 -92.87 -22.90 REMARK 500 SER B 249 -31.78 168.47 REMARK 500 SER B 250 91.77 83.13 REMARK 500 TYR B 269 -1.57 77.52 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 A 371 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 1 O REMARK 620 2 TRP A 1 N 70.8 REMARK 620 3 HIS A 11 NE2 92.5 113.4 REMARK 620 4 ASP A 130 OD2 164.8 94.0 94.9 REMARK 620 5 HOH A 421 O 82.8 115.0 126.4 103.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 372 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 56 OD1 REMARK 620 2 HIS A 126 NE2 88.9 REMARK 620 3 ASP A 130 OD1 170.8 94.5 REMARK 620 4 HOH A 421 O 76.6 121.1 108.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 373 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 136 NE2 REMARK 620 2 HIS A 148 NE2 95.5 REMARK 620 3 GLU A 152 OE2 148.6 92.0 REMARK 620 4 GLU A 152 OE1 94.8 104.5 53.9 REMARK 620 5 HOH A 374 O 100.0 77.1 111.3 164.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 374 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP B 1 O REMARK 620 2 TRP B 1 N 72.7 REMARK 620 3 HIS B 11 NE2 87.2 111.9 REMARK 620 4 ASP B 130 OD2 164.4 93.1 104.4 REMARK 620 5 HOH B 424 O 84.9 108.3 134.4 93.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 375 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 56 OD1 REMARK 620 2 HIS B 126 NE2 90.6 REMARK 620 3 ASP B 130 OD1 165.3 82.1 REMARK 620 4 HOH B 424 O 81.7 135.3 112.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 376 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 136 NE2 REMARK 620 2 HIS B 148 NE2 97.3 REMARK 620 3 GLU B 152 OE1 96.9 99.7 REMARK 620 4 GLU B 152 OE2 149.8 83.1 53.7 REMARK 620 N 1 2 3 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 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 373 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 374 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 375 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 376 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CA1 RELATED DB: PDB REMARK 900 ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS REMARK 900 RELATED ID: 1QM6 RELATED DB: PDB REMARK 900 R32 FORM OF CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN STRAIN REMARK 900 RELATED ID: 1QMD RELATED DB: PDB REMARK 900 CALCIUM BOUND CLOSED FORM ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS DBREF 1KHO A 1 370 UNP Q9RF12 PHLC2_CLOPE 29 398 DBREF 1KHO B 1 370 UNP Q9RF12 PHLC2_CLOPE 29 398 SEQRES 1 A 370 TRP ASP GLY LYS ALA ASP GLY THR GLY THR HIS ALA MET SEQRES 2 A 370 ILE ALA THR GLN GLY VAL THR ILE LEU GLU ASN ASP LEU SEQRES 3 A 370 SER SER ASN GLU PRO GLU VAL ILE ARG ASN ASN LEU GLU SEQRES 4 A 370 ILE LEU LYS GLN ASN MET HIS ASP 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 THR LYS ASP SER LYS TRP TYR LEU SER TYR SER ILE PRO SEQRES 8 A 370 ASP THR ALA GLU SER GLN ILE ARG LYS PHE SER ALA LEU SEQRES 9 A 370 ALA ARG TYR GLU TRP LYS 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 ALA ASP THR PRO TYR HIS ALA ALA ASN VAL THR ALA VAL SEQRES 12 A 370 ASP SER PRO GLY HIS VAL LYS PHE GLU THR PHE ALA GLU SEQRES 13 A 370 ASP ARG LYS ASP GLN TYR LYS ILE ASN THR THR GLY SER SEQRES 14 A 370 LYS THR ASN ASP ALA PHE TYR SER ASN ILE LEU THR ASN SEQRES 15 A 370 GLU ASP PHE ASN SER TRP SER LYS GLU PHE ALA ARG SER SEQRES 16 A 370 PHE ALA LYS THR ALA LYS ASP LEU TYR TYR SER HIS ALA SEQRES 17 A 370 ASN MET SER CYS SER TRP ASP GLU TRP ASP TYR ALA ALA SEQRES 18 A 370 LYS VAL ALA LEU ALA ASN SER GLN LYS GLY THR SER GLY SEQRES 19 A 370 TYR ILE TYR ARG PHE LEU HIS ASP VAL SER ASP GLY LYS SEQRES 20 A 370 ASP SER SER ALA ASN LYS ASN VAL ASN GLU LEU VAL ALA SEQRES 21 A 370 TYR ILE THR THR GLY GLY GLU LYS TYR ALA GLY THR ASP SEQRES 22 A 370 ASP TYR MET TYR PHE GLY ILE LYS THR LYS ASP GLY GLN SEQRES 23 A 370 THR GLN GLU TRP THR MET ASP ASN PRO GLY ASN ASP PHE SEQRES 24 A 370 MET THR GLY SER GLN ASP THR TYR THR PHE LYS LEU LYS SEQRES 25 A 370 ASP LYS ASN LEU LYS ILE ASP ASP ILE GLN ASN MET TRP SEQRES 26 A 370 ILE ARG LYS SER LYS TYR THR GLU PHE GLY ASP ASP TYR SEQRES 27 A 370 LYS PRO ALA ASN ILE LYS VAL ILE ALA ASN GLY ASN VAL SEQRES 28 A 370 VAL LEU ASN LYS ASP ILE ASN GLU TRP ILE SER GLY ASN SEQRES 29 A 370 SER THR TYR ASN ILE LYS SEQRES 1 B 370 TRP ASP GLY LYS ALA ASP GLY THR GLY THR HIS ALA MET SEQRES 2 B 370 ILE ALA THR GLN GLY VAL THR ILE LEU GLU ASN ASP LEU SEQRES 3 B 370 SER SER ASN GLU PRO GLU VAL ILE ARG ASN ASN LEU GLU SEQRES 4 B 370 ILE LEU LYS GLN ASN MET HIS ASP LEU GLN LEU GLY SER SEQRES 5 B 370 THR TYR PRO ASP TYR ASP LYS ASN ALA TYR ASP LEU TYR SEQRES 6 B 370 GLN ASP HIS PHE TRP ASP PRO ASP THR ASP ASN ASN PHE SEQRES 7 B 370 THR LYS ASP SER LYS TRP TYR LEU SER TYR SER ILE PRO SEQRES 8 B 370 ASP THR ALA GLU SER GLN ILE ARG LYS PHE SER ALA LEU SEQRES 9 B 370 ALA ARG TYR GLU TRP LYS ARG GLY ASN TYR LYS GLN ALA SEQRES 10 B 370 THR PHE TYR LEU GLY GLU ALA MET HIS TYR PHE GLY ASP SEQRES 11 B 370 ALA ASP THR PRO TYR HIS ALA ALA ASN VAL THR ALA VAL SEQRES 12 B 370 ASP SER PRO GLY HIS VAL LYS PHE GLU THR PHE ALA GLU SEQRES 13 B 370 ASP ARG LYS ASP GLN TYR LYS ILE ASN THR THR GLY SER SEQRES 14 B 370 LYS THR ASN ASP ALA PHE TYR SER ASN ILE LEU THR ASN SEQRES 15 B 370 GLU ASP PHE ASN SER TRP SER LYS GLU PHE ALA ARG SER SEQRES 16 B 370 PHE ALA LYS THR ALA LYS ASP LEU TYR TYR SER HIS ALA SEQRES 17 B 370 ASN MET SER CYS SER TRP ASP GLU TRP ASP TYR ALA ALA SEQRES 18 B 370 LYS VAL ALA LEU ALA ASN SER GLN LYS GLY THR SER GLY SEQRES 19 B 370 TYR ILE TYR ARG PHE LEU HIS ASP VAL SER ASP GLY LYS SEQRES 20 B 370 ASP SER SER ALA ASN LYS ASN VAL ASN GLU LEU VAL ALA SEQRES 21 B 370 TYR ILE THR THR GLY GLY GLU LYS TYR ALA GLY THR ASP SEQRES 22 B 370 ASP TYR MET TYR PHE GLY ILE LYS THR LYS ASP GLY GLN SEQRES 23 B 370 THR GLN GLU TRP THR MET ASP ASN PRO GLY ASN ASP PHE SEQRES 24 B 370 MET THR GLY SER GLN ASP THR TYR THR PHE LYS LEU LYS SEQRES 25 B 370 ASP LYS ASN LEU LYS ILE ASP ASP ILE GLN ASN MET TRP SEQRES 26 B 370 ILE ARG LYS SER LYS TYR THR GLU PHE GLY ASP ASP TYR SEQRES 27 B 370 LYS PRO ALA ASN ILE LYS VAL ILE ALA ASN GLY ASN VAL SEQRES 28 B 370 VAL LEU ASN LYS ASP ILE ASN GLU TRP ILE SER GLY ASN SEQRES 29 B 370 SER THR TYR ASN ILE LYS HET ZN A 371 1 HET ZN A 372 1 HET ZN A 373 1 HET ZN B 374 1 HET ZN B 375 1 HET ZN B 376 1 HETNAM ZN ZINC ION FORMUL 3 ZN 6(ZN 2+) FORMUL 9 HOH *152(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 SER A 82 SER A 87 5 6 HELIX 7 7 THR A 93 ARG A 111 1 19 HELIX 8 8 ASN A 113 ASP A 132 1 20 HELIX 9 9 THR A 133 ALA A 138 1 6 HELIX 10 10 PRO A 146 ARG A 158 1 13 HELIX 11 11 LYS A 159 LYS A 163 5 5 HELIX 12 12 ASP A 173 THR A 181 1 9 HELIX 13 13 ASP A 184 HIS A 207 1 24 HELIX 14 14 SER A 213 ASP A 245 1 33 HELIX 15 15 LYS A 317 ASP A 319 5 3 HELIX 16 16 GLY B 9 LEU B 26 1 18 HELIX 17 17 PRO B 31 ASN B 44 1 14 HELIX 18 18 ASN B 44 TYR B 54 1 11 HELIX 19 19 PRO B 55 TYR B 57 5 3 HELIX 20 20 TYR B 65 PHE B 69 5 5 HELIX 21 21 SER B 82 SER B 87 5 6 HELIX 22 22 THR B 93 GLY B 112 1 20 HELIX 23 23 ASN B 113 ASP B 132 1 20 HELIX 24 24 THR B 133 ALA B 138 1 6 HELIX 25 25 PRO B 146 ARG B 158 1 13 HELIX 26 26 LYS B 159 LYS B 163 5 5 HELIX 27 27 ASP B 173 THR B 181 1 9 HELIX 28 28 ASP B 184 HIS B 207 1 24 HELIX 29 29 SER B 213 ASP B 245 1 33 HELIX 30 30 LYS B 317 ASP B 319 5 3 SHEET 1 A 4 GLN A 304 LYS A 310 0 SHEET 2 A 4 GLU A 257 THR A 264 -1 N LEU A 258 O PHE A 309 SHEET 3 A 4 PRO A 340 ALA A 347 -1 O ILE A 346 N VAL A 259 SHEET 4 A 4 ASN A 350 ASP A 356 -1 O LYS A 355 N ILE A 343 SHEET 1 B 4 THR A 287 THR A 291 0 SHEET 2 B 4 TYR A 275 THR A 282 -1 N PHE A 278 O TRP A 290 SHEET 3 B 4 ILE A 321 SER A 329 -1 O TRP A 325 N GLY A 279 SHEET 4 B 4 SER A 365 ASN A 368 -1 O SER A 365 N LYS A 328 SHEET 1 C 4 GLN B 304 LYS B 310 0 SHEET 2 C 4 GLU B 257 THR B 264 -1 N LEU B 258 O PHE B 309 SHEET 3 C 4 PRO B 340 ALA B 347 -1 O ILE B 346 N VAL B 259 SHEET 4 C 4 ASN B 350 ASP B 356 -1 O ASN B 350 N ALA B 347 SHEET 1 D 4 THR B 287 THR B 291 0 SHEET 2 D 4 TYR B 275 THR B 282 -1 N PHE B 278 O TRP B 290 SHEET 3 D 4 ILE B 321 SER B 329 -1 O ARG B 327 N TYR B 277 SHEET 4 D 4 SER B 365 ASN B 368 -1 O TYR B 367 N ILE B 326 LINK O TRP A 1 ZN ZN A 371 1555 1555 2.44 LINK N TRP A 1 ZN ZN A 371 1555 1555 2.30 LINK NE2 HIS A 11 ZN ZN A 371 1555 1555 2.23 LINK OD1 ASP A 56 ZN ZN A 372 1555 1555 2.50 LINK NE2 HIS A 126 ZN ZN A 372 1555 1555 2.26 LINK OD2 ASP A 130 ZN ZN A 371 1555 1555 2.33 LINK OD1 ASP A 130 ZN ZN A 372 1555 1555 2.32 LINK NE2 HIS A 136 ZN ZN A 373 1555 1555 2.33 LINK NE2 HIS A 148 ZN ZN A 373 1555 1555 2.32 LINK OE2 GLU A 152 ZN ZN A 373 1555 1555 2.55 LINK OE1 GLU A 152 ZN ZN A 373 1555 1555 2.31 LINK ZN ZN A 371 O HOH A 421 1555 1555 2.40 LINK ZN ZN A 372 O HOH A 421 1555 1555 2.34 LINK ZN ZN A 373 O HOH A 374 1555 1555 2.49 LINK O TRP B 1 ZN ZN B 374 1555 1555 2.32 LINK N TRP B 1 ZN ZN B 374 1555 1555 2.43 LINK NE2 HIS B 11 ZN ZN B 374 1555 1555 2.20 LINK OD1 ASP B 56 ZN ZN B 375 1555 1555 2.53 LINK NE2 HIS B 126 ZN ZN B 375 1555 1555 2.20 LINK OD2 ASP B 130 ZN ZN B 374 1555 1555 2.35 LINK OD1 ASP B 130 ZN ZN B 375 1555 1555 2.36 LINK NE2 HIS B 136 ZN ZN B 376 1555 1555 2.27 LINK NE2 HIS B 148 ZN ZN B 376 1555 1555 2.29 LINK OE1 GLU B 152 ZN ZN B 376 1555 1555 2.38 LINK OE2 GLU B 152 ZN ZN B 376 1555 1555 2.48 LINK ZN ZN B 374 O HOH B 424 1555 1555 2.57 LINK ZN ZN B 375 O HOH B 424 1555 1555 2.53 SITE 1 AC1 5 TRP A 1 HIS A 11 ASP A 130 ZN A 372 SITE 2 AC1 5 HOH A 421 SITE 1 AC2 6 ASP A 56 HIS A 68 HIS A 126 ASP A 130 SITE 2 AC2 6 ZN A 371 HOH A 421 SITE 1 AC3 4 HIS A 136 HIS A 148 GLU A 152 HOH A 374 SITE 1 AC4 5 TRP B 1 HIS B 11 ASP B 130 ZN B 375 SITE 2 AC4 5 HOH B 424 SITE 1 AC5 6 ASP B 56 HIS B 68 HIS B 126 ASP B 130 SITE 2 AC5 6 ZN B 374 HOH B 424 SITE 1 AC6 4 HIS B 136 HIS B 148 GLU B 152 HOH B 377 CRYST1 117.230 117.230 220.590 90.00 90.00 90.00 P 41 2 2 16 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 0.008530 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008530 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004533 0.00000