HEADER TOXIN 23-AUG-06 2J3X TITLE CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONENT C2-I OF THE C2-TOXIN FROM TITLE 2 CLOSTRIDIUM BOTULINUM AT PH 3.0 (MUT-S361R) COMPND MOL_ID: 1; COMPND 2 MOLECULE: C2 TOXIN COMPONENT I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADP-RIBOSYLTRANSFERASE C2-I; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM BOTULINUM; SOURCE 3 ORGANISM_TAXID: 1491; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-3B KEYWDS ADP-RIBOSYLTRANSFERASE, TOXIN, CLOSTRIDIUM BOTULINUM EXPDTA X-RAY DIFFRACTION AUTHOR C.SCHLEBERGER,H.HOCHMANN,H.BARTH,K.AKTORIES,G.E.SCHULZ REVDAT 5 13-DEC-23 2J3X 1 REMARK REVDAT 4 08-MAY-19 2J3X 1 REMARK REVDAT 3 24-FEB-09 2J3X 1 VERSN REVDAT 2 30-NOV-06 2J3X 1 JRNL REVDAT 1 11-OCT-06 2J3X 0 JRNL AUTH C.SCHLEBERGER,H.HOCHMANN,H.BARTH,K.AKTORIES,G.E.SCHULZ JRNL TITL STRUCTURE AND ACTION OF THE BINARY C2 TOXIN FROM CLOSTRIDIUM JRNL TITL 2 BOTULINUM. JRNL REF J.MOL.BIOL. V. 364 705 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 17027031 JRNL DOI 10.1016/J.JMB.2006.09.002 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 60575 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2523 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4278 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3479 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 116 REMARK 3 SOLVENT ATOMS : 524 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.33000 REMARK 3 B22 (A**2) : 0.33000 REMARK 3 B33 (A**2) : -0.50000 REMARK 3 B12 (A**2) : 0.17000 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): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.834 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3785 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5127 ; 1.780 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 472 ; 5.922 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;31.476 ;25.744 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 712 ;14.122 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.008 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 558 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2812 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1841 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2596 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 449 ; 0.187 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 102 ; 0.236 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 42 ; 0.216 ; 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): 2288 ; 1.279 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3620 ; 2.011 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1683 ; 2.918 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1485 ; 4.494 ; 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 : BABINET MODEL WITH 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 2J3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1290029818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 3.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63100 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 48.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2J3V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 10 MG/ML RESERVOIR: 0.1 M REMARK 280 CITRAT PH 3.0, 0.8 M (NH4)2SO4 HANGING DROP 1:1, PH 3.00, VAPOR REMARK 280 DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 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 0.00000 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 81.41500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 81.41500 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 81.41500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 81.41500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 81.41500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 81.41500 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: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2086 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 20 TO GLU REMARK 400 ENGINEERED RESIDUE IN CHAIN A, SER 361 TO ARG REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 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 OE1 GLU A 244 O HOH A 2287 1.87 REMARK 500 OE2 GLU A 232 O HOH A 2274 2.10 REMARK 500 OD1 ASP A 307 O HOH A 2360 2.13 REMARK 500 NZ LYS A 19 O LYS A 180 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CD1 ILE A 3 O HOH A 2080 2665 2.05 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 A 171 -13.76 83.77 REMARK 500 ASP A 179 -150.09 -116.88 REMARK 500 TYR A 222 -133.85 47.66 REMARK 500 SER A 226 97.24 -161.01 REMARK 500 SER A 255 -35.51 -136.50 REMARK 500 ASP A 302 -159.98 -97.02 REMARK 500 ASN A 428 130.93 -39.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1443 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1444 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1445 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1446 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1447 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1448 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1449 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1451 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1452 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1432 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1433 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1434 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1435 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1436 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1437 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1438 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1439 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1440 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1441 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1442 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2J3V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONENT C2-I OF THE C2-TOXIN REMARK 900 FROM CLOSTRIDIUM BOTULINUM AT PH 3.0 REMARK 900 RELATED ID: 2J3Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EZYMATIC COMPONENT C2-I OF THE C2-TOXIN REMARK 900 FROM CLOSTRIDIUM BOTULINUM AT PH 6.1 REMARK 900 RELATED ID: 2J42 RELATED DB: PDB REMARK 900 LOW QUALITY CRYSTAL STRUCTURE OF THE TRANSPORT COMPONENT C2-II OF REMARK 900 THE C2-TOXIN FROM CLOSTRIDIUM BOTULINUM DBREF 2J3X A 1 431 UNP O69275 O69275_CLOBO 1 431 SEQADV 2J3X GLU A 20 UNP O69275 LYS 20 ENGINEERED MUTATION SEQADV 2J3X GLN A 77 UNP O69275 HIS 77 CONFLICT SEQADV 2J3X ASP A 121 UNP O69275 ASN 121 CONFLICT SEQADV 2J3X ARG A 361 UNP O69275 SER 361 ENGINEERED MUTATION SEQRES 1 A 431 MET PRO ILE ILE LYS GLU PRO ILE ASP PHE ILE ASN LYS SEQRES 2 A 431 PRO GLU SER GLU ALA LYS GLU TRP GLY LYS GLU GLU GLU SEQRES 3 A 431 LYS ARG TRP PHE THR LYS LEU ASN ASN LEU GLU GLU VAL SEQRES 4 A 431 ALA VAL ASN GLN LEU LYS ASN LYS GLU TYR LYS THR LYS SEQRES 5 A 431 ILE ASP ASN PHE SER THR ASP ILE LEU PHE SER SER LEU SEQRES 6 A 431 THR ALA ILE GLU ILE MET LYS GLU ASP GLU ASN GLN ASN SEQRES 7 A 431 LEU PHE ASP VAL GLU ARG ILE ARG GLU ALA LEU LEU LYS SEQRES 8 A 431 ASN THR LEU ASP ARG ASP ALA ILE GLY TYR VAL ASN PHE SEQRES 9 A 431 THR PRO LYS GLU LEU GLY ILE ASN PHE SER ILE ARG ASP SEQRES 10 A 431 VAL GLU LEU ASP ARG ASP ILE SER ASP GLU THR LEU ASP SEQRES 11 A 431 LYS VAL ARG GLN GLN ILE ILE ASN GLN GLU TYR THR LYS SEQRES 12 A 431 PHE SER PHE ILE SER LEU GLY LEU ASN ASP ASN SER ILE SEQRES 13 A 431 ASN GLU SER VAL PRO VAL ILE VAL LYS THR ARG VAL PRO SEQRES 14 A 431 THR THR PHE ASP TYR GLY VAL LEU ASN ASP LYS GLU THR SEQRES 15 A 431 VAL SER LEU LEU LEU ASN GLN GLY PHE SER ILE ILE PRO SEQRES 16 A 431 GLU SER ALA ILE ILE THR THR ILE LYS GLY LYS ASP TYR SEQRES 17 A 431 ILE LEU ILE GLU GLY SER LEU SER GLN GLU LEU ASP PHE SEQRES 18 A 431 TYR ASN LYS GLY SER GLU ALA TRP GLY ALA GLU ASN TYR SEQRES 19 A 431 GLY ASP TYR ILE SER LYS LEU SER HIS GLU GLN LEU GLY SEQRES 20 A 431 ALA LEU GLU GLY TYR LEU HIS SER ASP TYR LYS ALA ILE SEQRES 21 A 431 ASN SER TYR LEU ARG ASN ASN ARG VAL PRO ASN ASN ASP SEQRES 22 A 431 GLU LEU ASN LYS LYS ILE GLU LEU ILE SER SER ALA LEU SEQRES 23 A 431 SER VAL LYS PRO ILE PRO GLN THR LEU ILE ALA TYR ARG SEQRES 24 A 431 ARG VAL ASP GLY ILE PRO PHE ASP LEU PRO SER ASP PHE SEQRES 25 A 431 SER PHE ASP LYS LYS GLU ASN GLY GLU ILE ILE ALA ASP SEQRES 26 A 431 LYS GLN LYS LEU ASN GLU PHE ILE ASP LYS TRP THR GLY SEQRES 27 A 431 LYS GLU ILE GLU ASN LEU SER PHE SER SER THR SER LEU SEQRES 28 A 431 LYS SER THR PRO SER SER PHE SER LYS ARG ARG PHE ILE SEQRES 29 A 431 PHE ARG LEU ARG LEU SER GLU GLY ALA ILE GLY ALA PHE SEQRES 30 A 431 ILE TYR GLY PHE SER GLY PHE GLN ASP GLU GLN GLU ILE SEQRES 31 A 431 LEU LEU ASN LYS ASN SER THR PHE LYS ILE PHE ARG ILE SEQRES 32 A 431 THR PRO ILE THR SER ILE ILE ASN ARG VAL THR LYS MET SEQRES 33 A 431 THR GLN VAL VAL ILE ASP ALA GLU GLY ILE GLN ASN LYS SEQRES 34 A 431 GLU ILE HET GOL A1432 6 HET GOL A1433 6 HET GOL A1434 6 HET GOL A1435 6 HET GOL A1436 6 HET GOL A1437 6 HET GOL A1438 6 HET GOL A1439 6 HET GOL A1440 6 HET GOL A1441 6 HET GOL A1442 6 HET SO4 A1443 5 HET SO4 A1444 5 HET SO4 A1445 5 HET SO4 A1446 5 HET SO4 A1447 5 HET SO4 A1448 5 HET SO4 A1449 5 HET SO4 A1450 5 HET SO4 A1451 5 HET SO4 A1452 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 11(C3 H8 O3) FORMUL 13 SO4 10(O4 S 2-) FORMUL 23 HOH *524(H2 O) HELIX 1 1 GLU A 15 LYS A 32 1 18 HELIX 2 2 ASN A 35 LYS A 45 1 11 HELIX 3 3 LYS A 47 LEU A 61 1 15 HELIX 4 4 LEU A 65 GLU A 75 1 11 HELIX 5 5 GLN A 77 ASN A 92 1 16 HELIX 6 6 PRO A 106 GLY A 110 5 5 HELIX 7 7 ASP A 126 ILE A 137 1 12 HELIX 8 8 ASP A 153 ILE A 156 5 4 HELIX 9 9 GLU A 227 ASP A 236 1 10 HELIX 10 10 ILE A 238 LEU A 241 1 4 HELIX 11 11 HIS A 243 SER A 255 1 13 HELIX 12 12 ASP A 256 ASN A 267 1 12 HELIX 13 13 ASP A 273 VAL A 288 1 16 HELIX 14 14 ILE A 304 ASP A 307 5 4 HELIX 15 15 LYS A 326 THR A 337 1 12 HELIX 16 16 SER A 356 SER A 359 5 4 SHEET 1 AA 5 ALA A 98 VAL A 102 0 SHEET 2 AA 5 VAL A 162 VAL A 168 -1 O VAL A 164 N VAL A 102 SHEET 3 AA 5 LYS A 206 GLN A 217 1 O ILE A 209 N ILE A 163 SHEET 4 AA 5 PHE A 191 ILE A 203 -1 O SER A 192 N SER A 216 SHEET 5 AA 5 TYR A 141 LYS A 143 -1 O TYR A 141 N ILE A 193 SHEET 1 AB 3 ILE A 147 GLY A 150 0 SHEET 2 AB 3 VAL A 183 LEU A 187 -1 O VAL A 183 N LEU A 151 SHEET 3 AB 3 GLY A 175 ASN A 178 0 SHEET 1 AC 5 LEU A 295 VAL A 301 0 SHEET 2 AC 5 PHE A 363 LEU A 369 -1 O PHE A 363 N VAL A 301 SHEET 3 AC 5 THR A 414 ILE A 426 1 O VAL A 419 N ILE A 364 SHEET 4 AC 5 SER A 396 ASN A 411 -1 O THR A 397 N ILE A 426 SHEET 5 AC 5 LYS A 339 ASN A 343 -1 O ILE A 341 N PHE A 398 SHEET 1 AD 2 ASP A 315 GLU A 318 0 SHEET 2 AD 2 GLU A 321 ALA A 324 -1 O GLU A 321 N GLU A 318 SHEET 1 AE 3 SER A 347 SER A 350 0 SHEET 2 AE 3 GLU A 389 LEU A 392 -1 O ILE A 390 N THR A 349 SHEET 3 AE 3 GLY A 375 PHE A 377 -1 O ALA A 376 N LEU A 391 CISPEP 1 VAL A 269 PRO A 270 0 1.45 SITE 1 AC1 10 LYS A 72 GLU A 83 ARG A 86 LYS A 224 SITE 2 AC1 10 GLY A 235 TYR A 379 GOL A1433 HOH A2272 SITE 3 AC1 10 HOH A2483 HOH A2503 SITE 1 AC2 7 PRO A 14 GLU A 15 SER A 16 ILE A 426 SITE 2 AC2 7 GLN A 427 HOH A2504 HOH A2505 SITE 1 AC3 9 SER A 114 ILE A 115 ARG A 116 LYS A 328 SITE 2 AC3 9 HOH A2384 HOH A2391 HOH A2506 HOH A2507 SITE 3 AC3 9 HOH A2508 SITE 1 AC4 8 LYS A 50 THR A 51 ASP A 54 ASN A 103 SITE 2 AC4 8 HOH A2059 HOH A2509 HOH A2510 HOH A2511 SITE 1 AC5 5 LYS A 131 LYS A 335 HOH A2512 HOH A2513 SITE 2 AC5 5 HOH A2515 SITE 1 AC6 4 LYS A 339 GLU A 340 HOH A2402 HOH A2516 SITE 1 AC7 4 ASN A 34 ASN A 35 HOH A2517 HOH A2518 SITE 1 AC8 7 TRP A 21 GLU A 25 ARG A 28 ASP A 95 SITE 2 AC8 7 ARG A 96 GLU A 371 HOH A2114 SITE 1 AC9 8 THR A 66 GLU A 69 SER A 382 GLY A 383 SITE 2 AC9 8 GLN A 385 HOH A2519 HOH A2520 HOH A2521 SITE 1 BC1 6 SER A 226 GLU A 227 ALA A 228 HOH A2267 SITE 2 BC1 6 HOH A2522 HOH A2523 SITE 1 BC2 6 ARG A 299 ARG A 300 SER A 348 PHE A 358 SITE 2 BC2 6 GOL A1434 HOH A2482 SITE 1 BC3 8 ILE A 60 ILE A 68 LEU A 79 ARG A 86 SITE 2 BC3 8 ASN A 223 GOL A1436 SO4 A1443 HOH A2483 SITE 1 BC4 6 ARG A 299 SER A 347 SER A 348 ARG A 361 SITE 2 BC4 6 GOL A1432 HOH A2295 SITE 1 BC5 9 ASN A 34 GLU A 37 GLU A 87 LYS A 91 SITE 2 BC5 9 LYS A 240 HOH A2340 HOH A2484 HOH A2485 SITE 3 BC5 9 HOH A2518 SITE 1 BC6 6 ARG A 86 LYS A 224 GOL A1433 HOH A2488 SITE 2 BC6 6 HOH A2489 HOH A2490 SITE 1 BC7 5 ASP A 59 THR A 407 HOH A2457 HOH A2491 SITE 2 BC7 5 HOH A2492 SITE 1 BC8 10 ASN A 55 THR A 58 GLU A 108 THR A 142 SITE 2 BC8 10 LYS A 143 PHE A 144 SER A 145 HOH A2493 SITE 3 BC8 10 HOH A2494 HOH A2495 SITE 1 BC9 9 THR A 66 LYS A 352 PRO A 355 SER A 356 SITE 2 BC9 9 GLN A 385 HOH A2414 HOH A2433 HOH A2496 SITE 3 BC9 9 HOH A2498 SITE 1 CC1 9 ARG A 299 PRO A 305 ILE A 341 ASN A 343 SITE 2 CC1 9 PHE A 365 PHE A 398 HOH A2411 HOH A2499 SITE 3 CC1 9 HOH A2500 SITE 1 CC2 5 ARG A 361 HOH A2352 HOH A2353 HOH A2416 SITE 2 CC2 5 HOH A2501 SITE 1 CC3 3 GLN A 293 THR A 294 HOH A2348 CRYST1 115.720 115.720 162.830 90.00 90.00 120.00 P 63 2 2 12 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 0.008642 0.004989 0.000000 0.00000 SCALE2 0.000000 0.009978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006141 0.00000