HEADER HYDROLASE/HYDROLASE INHIBITOR 17-MAY-13 4KS6 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN TITLE 2 BONT/A C134S MUTANT WITH COVALENT INHIBITOR THAT MODIFIES CYS-165 TITLE 3 CAUSING DISORDER IN 166-174 STRETCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: BOTULINUM NEUROTOXIN A LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN RESIDUES 1-425; COMPND 5 SYNONYM: BOTULINUM NEUROTOXIN TYPE A, BONT/A, BONTOXILYSIN-A, BOTOX; COMPND 6 EC: 3.4.24.69; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PEPTIDE INHIBITOR MPT-DPP-DAR-G-DPN-NH2; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM BOTULINUM A; SOURCE 3 ORGANISM_TAXID: 441771; SOURCE 4 STRAIN: STRAIN HALL / ATCC 3502 / NCTC 13319 / TYPE A; SOURCE 5 GENE: BOTA, CBO0806, CLC_0862; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A+; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS CLOSTRIDIAL NEUROTOXIN ZINC PROTEASE, PEPTIDASE_M27, SNAP 25, KEYWDS 2 COVALENT INHIBITION, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.A.STURA,L.VERA,K.GUITOT,V.DIVE REVDAT 3 20-SEP-23 4KS6 1 REMARK SEQADV LINK REVDAT 2 25-APR-18 4KS6 1 SOURCE REMARK REVDAT 1 25-JUN-14 4KS6 0 JRNL AUTH K.GUITOT,L.VERA,L.LE ROUX,S.BREGANT,D.PTCHELKINE,F.BEAU, JRNL AUTH 2 E.A.STURA,V.DIVE JRNL TITL COVALENT MODIFICATION OF THE ACTIVE SITE CYSTEINE STRESSES JRNL TITL 2 CLOSTRIDIUM BOTULINUM NEUROTOXIN A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 32454 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1724 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2322 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3502 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 374 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : -0.09000 REMARK 3 B33 (A**2) : 0.18000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.187 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.711 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3720 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5032 ; 1.514 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 6.166 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;38.606 ;25.027 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 627 ;14.553 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;13.167 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 538 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2861 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2191 ; 1.731 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3572 ; 2.691 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1529 ; 3.786 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1458 ; 5.592 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4KS6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97240 REMARK 200 MONOCHROMATOR : HORIZONTALLY DIFFRACTING SI REMARK 200 (111) MONOCHROMATOR AND PT REMARK 200 COATED MIRRORS IN KIRKPATRICK- REMARK 200 BAEZ GEOMETRY FOR FOCUSING REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42323 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 15.40 REMARK 200 R MERGE (I) : 0.37700 REMARK 200 R SYM (I) : 0.36500 REMARK 200 FOR THE DATA SET : 9.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 15.42 REMARK 200 R MERGE FOR SHELL (I) : 4.88600 REMARK 200 R SYM FOR SHELL (I) : 4.72600 REMARK 200 FOR SHELL : 0.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4ELC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN COMPLEX - 6 MICROL LCA C134S REMARK 280 AT 145 MICROM + 1.4 MICROL KG23 AT 1.25 MILLI-M, RESERVOIR - REMARK 280 17.5% PEG 600, 0.065 M HEPES PH 7.5. CRYOPROTECTANT - CRYOPROTX REMARK 280 CM1, 10% PEG 20K, 100 MILLIM CHC (CITRIC ACID, HEPES, CHES - 40% REMARK 280 PH 4 / 60% PH 10), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K, PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -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 100.86250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.81700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.81700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 151.29375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.81700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.81700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.43125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.81700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.81700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 151.29375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.81700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.81700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.43125 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 0.00000 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 100.86250 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 300 REMARK: ONE MONOMER IN THE ASYMMETRIC UNIT 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: 3410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 A 927 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 966 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE PEPTIDE INHIBITOR MPT-DPP-DAR-G-DPN-NH2 IS PEPTIDE-LIKE, A REMARK 400 MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: PEPTIDE INHIBITOR MPT-DPP-DAR-G-DPN-NH2 REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE A 38 CA CB CG1 CG2 CD1 REMARK 480 LYS A 66 CG 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 OG SER A 309 O HOH A 844 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 GLY A -2 N GLY A -2 CA 0.096 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 LEU A 173 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 DPN B 5 CA - CB - CG ANGL. DEV. = -20.3 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 VAL A 17 -73.75 -118.76 REMARK 500 GLN A 29 -7.08 75.37 REMARK 500 PRO A 54 6.26 -59.48 REMARK 500 GLU A 56 49.35 -102.99 REMARK 500 SER A 157 -153.51 -77.47 REMARK 500 SER A 167 -54.03 -145.18 REMARK 500 ASP A 275 118.01 -39.05 REMARK 500 ASN A 409 49.28 -98.72 REMARK 500 GLU A 424 -4.06 176.76 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 223 NE2 REMARK 620 2 HIS A 227 NE2 93.4 REMARK 620 3 GLU A 262 OE1 100.8 93.6 REMARK 620 4 GLU A 262 OE2 156.4 88.8 55.5 REMARK 620 5 DPP B 2 N 118.8 96.9 138.1 84.1 REMARK 620 6 DPP B 2 O 87.9 174.9 91.0 91.9 78.1 REMARK 620 N 1 2 3 4 5 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF PEPTIDE INHIBITOR REMARK 800 MPT-DPP-DAR-G-DPN-NH2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ELC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN REMARK 900 BONT/A C134 MUTANT WITH MTSEA MODIFIED CYS-165 REMARK 900 RELATED ID: 4EJ5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN REMARK 900 BONT/A WILD-TYPE REMARK 900 RELATED ID: 4EL4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN REMARK 900 BONT/A C134S/C165S DOUBLE MUTANT REMARK 900 RELATED ID: 4KTX RELATED DB: PDB DBREF 4KS6 A 1 425 UNP A5HZZ9 BXA1_CLOBH 1 425 DBREF 4KS6 B 1 6 PDB 4KS6 4KS6 1 6 SEQADV 4KS6 MET A -19 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 GLY A -18 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 SER A -17 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 SER A -16 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 HIS A -15 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 HIS A -14 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 HIS A -13 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 HIS A -12 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 HIS A -11 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 HIS A -10 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 SER A -9 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 SER A -8 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 GLY A -7 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 LEU A -6 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 VAL A -5 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 PRO A -4 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 ARG A -3 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 GLY A -2 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 SER A -1 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 HIS A 0 UNP A5HZZ9 EXPRESSION TAG SEQADV 4KS6 SER A 134 UNP A5HZZ9 CYS 134 ENGINEERED MUTATION SEQRES 1 A 445 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 445 LEU VAL PRO ARG GLY SER HIS MET PRO PHE VAL ASN LYS SEQRES 3 A 445 GLN PHE ASN TYR LYS ASP PRO VAL ASN GLY VAL ASP ILE SEQRES 4 A 445 ALA TYR ILE LYS ILE PRO ASN ALA GLY GLN MET GLN PRO SEQRES 5 A 445 VAL LYS ALA PHE LYS ILE HIS ASN LYS ILE TRP VAL ILE SEQRES 6 A 445 PRO GLU ARG ASP THR PHE THR ASN PRO GLU GLU GLY ASP SEQRES 7 A 445 LEU ASN PRO PRO PRO GLU ALA LYS GLN VAL PRO VAL SER SEQRES 8 A 445 TYR TYR ASP SER THR TYR LEU SER THR ASP ASN GLU LYS SEQRES 9 A 445 ASP ASN TYR LEU LYS GLY VAL THR LYS LEU PHE GLU ARG SEQRES 10 A 445 ILE TYR SER THR ASP LEU GLY ARG MET LEU LEU THR SER SEQRES 11 A 445 ILE VAL ARG GLY ILE PRO PHE TRP GLY GLY SER THR ILE SEQRES 12 A 445 ASP THR GLU LEU LYS VAL ILE ASP THR ASN SER ILE ASN SEQRES 13 A 445 VAL ILE GLN PRO ASP GLY SER TYR ARG SER GLU GLU LEU SEQRES 14 A 445 ASN LEU VAL ILE ILE GLY PRO SER ALA ASP ILE ILE GLN SEQRES 15 A 445 PHE GLU CYS LYS SER PHE GLY HIS GLU VAL LEU ASN LEU SEQRES 16 A 445 THR ARG ASN GLY TYR GLY SER THR GLN TYR ILE ARG PHE SEQRES 17 A 445 SER PRO ASP PHE THR PHE GLY PHE GLU GLU SER LEU GLU SEQRES 18 A 445 VAL ASP THR ASN PRO LEU LEU GLY ALA GLY LYS PHE ALA SEQRES 19 A 445 THR ASP PRO ALA VAL THR LEU ALA HIS GLU LEU ILE HIS SEQRES 20 A 445 ALA GLY HIS ARG LEU TYR GLY ILE ALA ILE ASN PRO ASN SEQRES 21 A 445 ARG VAL PHE LYS VAL ASN THR ASN ALA TYR TYR GLU MET SEQRES 22 A 445 SER GLY LEU GLU VAL SER PHE GLU GLU LEU ARG THR PHE SEQRES 23 A 445 GLY GLY HIS ASP ALA LYS PHE ILE ASP SER LEU GLN GLU SEQRES 24 A 445 ASN GLU PHE ARG LEU TYR TYR TYR ASN LYS PHE LYS ASP SEQRES 25 A 445 ILE ALA SER THR LEU ASN LYS ALA LYS SER ILE VAL GLY SEQRES 26 A 445 THR THR ALA SER LEU GLN TYR MET LYS ASN VAL PHE LYS SEQRES 27 A 445 GLU LYS TYR LEU LEU SER GLU ASP THR SER GLY LYS PHE SEQRES 28 A 445 SER VAL ASP LYS LEU LYS PHE ASP LYS LEU TYR LYS MET SEQRES 29 A 445 LEU THR GLU ILE TYR THR GLU ASP ASN PHE VAL LYS PHE SEQRES 30 A 445 PHE LYS VAL LEU ASN ARG LYS THR TYR LEU ASN PHE ASP SEQRES 31 A 445 LYS ALA VAL PHE LYS ILE ASN ILE VAL PRO LYS VAL ASN SEQRES 32 A 445 TYR THR ILE TYR ASP GLY PHE ASN LEU ARG ASN THR ASN SEQRES 33 A 445 LEU ALA ALA ASN PHE ASN GLY GLN ASN THR GLU ILE ASN SEQRES 34 A 445 ASN MET ASN PHE THR LYS LEU LYS ASN PHE THR GLY LEU SEQRES 35 A 445 PHE GLU PHE SEQRES 1 B 6 MPT DPP DAR GLY DPN NH2 MODRES 4KS6 DPP B 2 ALA DIAMINOPROPANOIC ACID HET MPT B 1 5 HET DPP B 2 6 HET DAR B 3 11 HET DPN B 5 11 HET NH2 B 6 1 HET ZN A 501 1 HET SO4 A 502 5 HET GOL A 503 6 HET GOL A 504 6 HET PEG A 505 7 HET PGO A 506 5 HET GOL A 507 6 HET PGO A 508 5 HET EDO A 509 4 HET EDO A 510 4 HET EDO A 511 4 HETNAM MPT BETA-MERCAPTOPROPIONIC ACID HETNAM DPP DIAMINOPROPANOIC ACID HETNAM DAR D-ARGININE HETNAM DPN D-PHENYLALANINE HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGO S-1,2-PROPANEDIOL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MPT C3 H6 O2 S FORMUL 2 DPP C3 H8 N2 O2 FORMUL 2 DAR C6 H15 N4 O2 1+ FORMUL 2 DPN C9 H11 N O2 FORMUL 2 NH2 H2 N FORMUL 3 ZN ZN 2+ FORMUL 4 SO4 O4 S 2- FORMUL 5 GOL 3(C3 H8 O3) FORMUL 7 PEG C4 H10 O3 FORMUL 8 PGO 2(C3 H8 O2) FORMUL 11 EDO 3(C2 H6 O2) FORMUL 14 HOH *374(H2 O) HELIX 1 1 PRO A 63 GLN A 67 5 5 HELIX 2 2 THR A 80 SER A 100 1 21 HELIX 3 3 THR A 101 GLY A 114 1 14 HELIX 4 4 ILE A 130 THR A 132 5 3 HELIX 5 5 VAL A 172 ARG A 177 5 6 HELIX 6 6 SER A 199 THR A 204 1 6 HELIX 7 7 ASP A 216 TYR A 233 1 18 HELIX 8 8 ASN A 248 MET A 253 1 6 HELIX 9 9 PHE A 260 GLY A 267 1 8 HELIX 10 10 HIS A 269 ILE A 274 5 6 HELIX 11 11 ASP A 275 ALA A 300 1 26 HELIX 12 12 SER A 309 TYR A 321 1 13 HELIX 13 13 ASP A 334 GLU A 347 1 14 HELIX 14 14 THR A 350 LYS A 359 1 10 HELIX 15 15 PHE A 401 ASN A 405 5 5 HELIX 16 16 ASN A 409 PHE A 413 5 5 SHEET 1 A 7 TYR A 144 GLU A 148 0 SHEET 2 A 7 SER A 134 ILE A 138 -1 N ILE A 135 O GLU A 147 SHEET 3 A 7 ILE A 19 LYS A 23 -1 N LYS A 23 O ASN A 136 SHEET 4 A 7 VAL A 33 HIS A 39 -1 O ALA A 35 N ALA A 20 SHEET 5 A 7 ILE A 42 ILE A 45 -1 O VAL A 44 N PHE A 36 SHEET 6 A 7 LEU A 151 ILE A 154 1 O ILE A 153 N ILE A 45 SHEET 7 A 7 GLN A 184 ARG A 187 1 O ILE A 186 N VAL A 152 SHEET 1 B 2 GLU A 126 LEU A 127 0 SHEET 2 B 2 SER A 302 ILE A 303 1 O SER A 302 N LEU A 127 SHEET 1 C 4 PHE A 213 ALA A 214 0 SHEET 2 C 4 PHE A 192 PHE A 196 -1 N PHE A 196 O PHE A 213 SHEET 3 C 4 ALA A 372 LYS A 375 -1 O PHE A 374 N THR A 193 SHEET 4 C 4 THR A 414 ASN A 418 -1 O LEU A 416 N VAL A 373 SHEET 1 D 2 VAL A 242 LYS A 244 0 SHEET 2 D 2 GLU A 257 SER A 259 -1 O VAL A 258 N PHE A 243 SHEET 1 E 2 SER A 324 GLU A 325 0 SHEET 2 E 2 PHE A 331 SER A 332 -1 O SER A 332 N SER A 324 LINK SG CYS A 165 SG MPT B 1 1555 1555 2.09 LINK C MPT B 1 NG DPP B 2 1555 1555 1.33 LINK C DPP B 2 N DAR B 3 1555 1555 1.31 LINK C DAR B 3 N GLY B 4 1555 1555 1.34 LINK C GLY B 4 N DPN B 5 1555 1555 1.34 LINK C DPN B 5 N NH2 B 6 1555 1555 1.34 LINK NE2 HIS A 223 ZN ZN A 501 1555 1555 2.15 LINK NE2 HIS A 227 ZN ZN A 501 1555 1555 2.25 LINK OE1 GLU A 262 ZN ZN A 501 1555 1555 1.99 LINK OE2 GLU A 262 ZN ZN A 501 1555 1555 2.55 LINK ZN ZN A 501 N DPP B 2 1555 1555 2.05 LINK ZN ZN A 501 O DPP B 2 1555 1555 2.38 SITE 1 AC1 4 HIS A 223 HIS A 227 GLU A 262 DPP B 2 SITE 1 AC2 3 LYS A 375 ILE A 376 THR A 414 SITE 1 AC3 5 ASP A 339 ASN A 400 ASN A 402 PGO A 506 SITE 2 AC3 5 HOH A 764 SITE 1 AC4 5 PRO A 140 ASP A 141 LYS A 415 LEU A 416 SITE 2 AC4 5 ASN A 418 SITE 1 AC5 4 LYS A 6 GLN A 7 PHE A 8 THR A 92 SITE 1 AC6 7 ARG A 283 LEU A 284 TYR A 287 PHE A 338 SITE 2 AC6 7 ASP A 339 GOL A 503 HOH A 943 SITE 1 AC7 4 ASN A 383 MET A 411 ASN A 412 HOH A 774 SITE 1 AC8 5 ASN A 238 PHE A 282 TYR A 285 TYR A 286 SITE 2 AC8 5 HOH A 941 SITE 1 AC9 2 GLN A 139 HOH A 660 SITE 1 BC1 4 ILE A 160 PHE A 188 SER A 189 HOH A 904 SITE 1 BC2 6 LYS A 212 ARG A 283 ASP A 339 ASN A 405 SITE 2 BC2 6 GLU A 407 HOH A 872 SITE 1 BC3 24 PHE A 163 GLU A 164 CYS A 165 PHE A 194 SITE 2 BC3 24 THR A 215 HIS A 223 GLU A 224 HIS A 227 SITE 3 BC3 24 TYR A 251 LEU A 256 GLU A 262 ARG A 363 SITE 4 BC3 24 TYR A 366 ASN A 368 PHE A 369 ASP A 370 SITE 5 BC3 24 ZN A 501 HOH A 782 HOH A 804 HOH A 811 SITE 6 BC3 24 HOH A 824 HOH A 825 HOH B 101 HOH B 102 CRYST1 65.634 65.634 201.725 90.00 90.00 90.00 P 43 21 2 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 0.015236 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015236 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004957 0.00000