HEADER HYDROLASE 03-NOV-14 4D59 TITLE CLOSTRIDIAL CYSTEINE PROTEASE CWP84 C116A AFTER PROPEPTIDE CLEAVAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED COMPND 3 CYSTEINE PROTEASE); COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: CYSTEINE PROTEASE DOMAIN, LECTIN-LIKE DOMAIN, RESIDUES 92- COMPND 6 497; COMPND 7 SYNONYM: CWP84; COMPND 8 EC: 3.4.22.15; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEPTOCLOSTRIDIUM DIFFICILE QCD-32G58; SOURCE 3 ORGANISM_TAXID: 367459; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS HYDROLASE, S-LAYER, SURFACE LAYER EXPDTA X-RAY DIFFRACTION AUTHOR W.J.BRADSHAW,A.K.ROBERTS,C.C.SHONE,K.R.ACHARYA REVDAT 4 20-DEC-23 4D59 1 REMARK LINK REVDAT 3 25-MAR-15 4D59 1 JRNL REVDAT 2 11-MAR-15 4D59 1 JRNL REVDAT 1 04-MAR-15 4D59 0 JRNL AUTH W.J.BRADSHAW,A.K.ROBERTS,C.C.SHONE,K.R.ACHARYA JRNL TITL CWP84, A CLOSTRIDIUM DIFFICILE CYSTEINE PROTEASE, EXHIBITS JRNL TITL 2 CONFORMATIONAL FLEXIBILITY IN THE ABSENCE OF ITS PROPEPTIDE JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 71 295 2015 JRNL REFN ESSN 1744-3091 JRNL PMID 25760704 JRNL DOI 10.1107/S2053230X15001065 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 82.2 REMARK 3 NUMBER OF REFLECTIONS : 55915 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2871 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) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4110 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.4440 REMARK 3 BIN FREE R VALUE SET COUNT : 189 REMARK 3 BIN FREE R VALUE : 0.4770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6350 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 449 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.42000 REMARK 3 B22 (A**2) : -1.70000 REMARK 3 B33 (A**2) : -3.72000 REMARK 3 B12 (A**2) : -0.40000 REMARK 3 B13 (A**2) : -1.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.223 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.237 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.065 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6570 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5949 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8926 ; 1.323 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13782 ; 0.753 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 826 ; 6.266 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 296 ;35.840 ;25.676 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1086 ;14.673 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;16.710 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 962 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7530 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1488 ; 0.001 ; 0.020 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): 3263 ; 1.696 ; 3.106 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3263 ; 1.695 ; 3.106 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4078 ; 2.593 ; 4.654 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3307 ; 1.627 ; 3.239 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 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. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 4D59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1290062201. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : SINGLE BOUNCE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 55.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.5 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4CI7 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% V/V DMSO, 20 % V/V JEFFAMINE REMARK 280 M2070, PH 8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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: 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 NZ LYS B 218 O HOH B 2128 2.05 REMARK 500 O LYS A 325 O HOH A 2026 2.09 REMARK 500 O HOH B 2004 O HOH B 2005 2.11 REMARK 500 OE1 GLU A 340 O HOH A 2131 2.13 REMARK 500 O HOH B 2128 O HOH B 2129 2.13 REMARK 500 OE1 GLU B 340 O HOH B 2183 2.14 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 TYR A 455 CA - CB - CG ANGL. DEV. = -11.4 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 261 9.73 -151.33 REMARK 500 SER A 294 -167.68 -106.59 REMARK 500 ALA A 342 128.70 -179.58 REMARK 500 SER A 397 62.36 -117.41 REMARK 500 SER B 93 159.26 -47.18 REMARK 500 SER B 164 -179.05 -64.66 REMARK 500 ASN B 261 13.81 -146.97 REMARK 500 ASN B 300 -168.90 -127.69 REMARK 500 THR B 314 -40.45 -132.23 REMARK 500 SER B 397 47.43 -140.09 REMARK 500 SER B 418 52.72 30.37 REMARK 500 ASP B 476 104.39 -53.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2092 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH B2152 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH B2256 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B2258 DISTANCE = 6.43 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 JEF A 1499 REMARK 610 JEF B 1499 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 CA A1498 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 339 O REMARK 620 2 GLU A 448 OE1 93.0 REMARK 620 3 LYS A 460 O 174.9 90.0 REMARK 620 4 ASN A 487 OD1 84.6 91.1 91.2 REMARK 620 5 JEF A1499 O 108.5 74.9 76.3 161.0 REMARK 620 6 JEF A1499 O10 74.7 132.0 106.3 132.0 66.3 REMARK 620 7 JEF A1499 O11 97.0 166.9 79.5 81.6 109.6 59.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1498 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 339 O REMARK 620 2 GLU B 448 OE1 90.0 REMARK 620 3 LYS B 460 O 169.6 99.7 REMARK 620 4 ASN B 487 OD1 95.2 88.8 88.5 REMARK 620 5 JEF B1499 O11 98.4 167.8 72.5 81.7 REMARK 620 6 JEF B1499 O10 75.8 130.7 94.9 138.7 60.6 REMARK 620 7 JEF B1499 O 107.3 78.4 71.6 153.8 107.3 62.3 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1498 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1498 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JEF A 1499 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JEF B 1499 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D5A RELATED DB: PDB REMARK 900 CLOSTRIDIAL CYSTEINE PROTEASE CWP84 C116A AFTER PROPEPTIDE CLEAVAGE REMARK 999 REMARK 999 SEQUENCE REMARK 999 STRUCTURE CONSISTS OF RESIDUES 92-497 WITH C116A. THE REMARK 999 SIGNAL PEPTIDE (1-32) AND CELL WALL BINDING DOMAINS (498- REMARK 999 803) WERE NOT PRESENT IN THE CONSTRUCT, THE PROPEPTIDE (33- REMARK 999 91) WAS CLEAVED BEFORE CRYSTALISATION. DBREF 4D59 A 92 497 UNP C9YQ11 C9YQ11_PEPDR 92 497 DBREF 4D59 B 92 497 UNP C9YQ11 C9YQ11_PEPDR 92 497 SEQADV 4D59 ALA A 116 UNP C9YQ11 CYS 116 ENGINEERED MUTATION SEQADV 4D59 ALA B 116 UNP C9YQ11 CYS 116 ENGINEERED MUTATION SEQRES 1 A 406 SER SER VAL ALA TYR ASN PRO MET ASP LEU GLY LEU THR SEQRES 2 A 406 THR PRO ALA LYS ASN GLN GLY SER LEU ASN THR ALA TRP SEQRES 3 A 406 SER PHE SER GLY MET SER THR LEU GLU ALA TYR LEU LYS SEQRES 4 A 406 LEU LYS GLY TYR GLY THR TYR ASP LEU SER GLU GLU HIS SEQRES 5 A 406 LEU ARG TRP TRP ALA THR GLY GLY LYS TYR GLY TRP ASN SEQRES 6 A 406 LEU ASP ASP MET SER GLY SER SER ASN VAL THR ALA ILE SEQRES 7 A 406 GLY TYR LEU THR ALA TRP ALA GLY PRO LYS LEU GLU LYS SEQRES 8 A 406 ASP ILE PRO TYR ASN LEU LYS SER GLU ALA GLN GLY ALA SEQRES 9 A 406 THR LYS PRO SER ASN MET ASP THR ALA PRO THR GLN PHE SEQRES 10 A 406 ASN VAL THR ASP VAL VAL ARG LEU ASN LYS ASP LYS GLU SEQRES 11 A 406 THR VAL LYS ASN ALA ILE MET GLN TYR GLY SER VAL THR SEQRES 12 A 406 SER GLY TYR ALA HIS TYR SER THR TYR PHE ASN LYS ASP SEQRES 13 A 406 GLU THR ALA TYR ASN CYS THR ASN LYS ARG ALA PRO LEU SEQRES 14 A 406 ASN HIS ALA VAL ALA ILE VAL GLY TRP ASP ASP ASN TYR SEQRES 15 A 406 SER LYS ASP ASN PHE ALA SER ASP VAL LYS PRO GLU SER SEQRES 16 A 406 ASN GLY ALA TRP LEU VAL LYS SER SER TRP GLY GLU PHE SEQRES 17 A 406 ASN SER MET LYS GLY PHE PHE TRP ILE SER TYR GLU ASP SEQRES 18 A 406 LYS THR LEU LEU THR ASP THR ASP ASN TYR ALA MET LYS SEQRES 19 A 406 SER VAL SER LYS PRO ASP SER ASP LYS LYS MET TYR GLN SEQRES 20 A 406 LEU GLU TYR ALA GLY LEU SER LYS ILE MET SER ASN LYS SEQRES 21 A 406 VAL THR ALA ALA ASN VAL PHE ASP PHE SER ARG ASP SER SEQRES 22 A 406 GLU LYS LEU ASP SER VAL MET PHE GLU THR ASP SER VAL SEQRES 23 A 406 GLY ALA LYS TYR GLU VAL TYR TYR ALA PRO VAL VAL ASN SEQRES 24 A 406 GLY VAL PRO GLN ASN ASN SER MET THR LYS LEU ALA SER SEQRES 25 A 406 GLY THR VAL SER TYR SER GLY TYR ILE ASN VAL PRO THR SEQRES 26 A 406 ASN SER TYR SER LEU PRO LYS GLY LYS GLY ALA ILE VAL SEQRES 27 A 406 VAL VAL ILE ASP ASN THR ALA ASN PRO ASN ARG GLU LYS SEQRES 28 A 406 SER THR LEU ALA TYR GLU THR ASP ILE ASP GLY TYR TYR SEQRES 29 A 406 LEU TYR GLU ALA LYS ALA ASN LEU GLY GLU SER TYR ILE SEQRES 30 A 406 LEU GLN ASN ASN LYS PHE GLU ASP ILE ASN THR TYR SER SEQRES 31 A 406 GLU PHE SER PRO CYS ASN PHE VAL ILE LYS ALA ILE THR SEQRES 32 A 406 LYS THR SER SEQRES 1 B 406 SER SER VAL ALA TYR ASN PRO MET ASP LEU GLY LEU THR SEQRES 2 B 406 THR PRO ALA LYS ASN GLN GLY SER LEU ASN THR ALA TRP SEQRES 3 B 406 SER PHE SER GLY MET SER THR LEU GLU ALA TYR LEU LYS SEQRES 4 B 406 LEU LYS GLY TYR GLY THR TYR ASP LEU SER GLU GLU HIS SEQRES 5 B 406 LEU ARG TRP TRP ALA THR GLY GLY LYS TYR GLY TRP ASN SEQRES 6 B 406 LEU ASP ASP MET SER GLY SER SER ASN VAL THR ALA ILE SEQRES 7 B 406 GLY TYR LEU THR ALA TRP ALA GLY PRO LYS LEU GLU LYS SEQRES 8 B 406 ASP ILE PRO TYR ASN LEU LYS SER GLU ALA GLN GLY ALA SEQRES 9 B 406 THR LYS PRO SER ASN MET ASP THR ALA PRO THR GLN PHE SEQRES 10 B 406 ASN VAL THR ASP VAL VAL ARG LEU ASN LYS ASP LYS GLU SEQRES 11 B 406 THR VAL LYS ASN ALA ILE MET GLN TYR GLY SER VAL THR SEQRES 12 B 406 SER GLY TYR ALA HIS TYR SER THR TYR PHE ASN LYS ASP SEQRES 13 B 406 GLU THR ALA TYR ASN CYS THR ASN LYS ARG ALA PRO LEU SEQRES 14 B 406 ASN HIS ALA VAL ALA ILE VAL GLY TRP ASP ASP ASN TYR SEQRES 15 B 406 SER LYS ASP ASN PHE ALA SER ASP VAL LYS PRO GLU SER SEQRES 16 B 406 ASN GLY ALA TRP LEU VAL LYS SER SER TRP GLY GLU PHE SEQRES 17 B 406 ASN SER MET LYS GLY PHE PHE TRP ILE SER TYR GLU ASP SEQRES 18 B 406 LYS THR LEU LEU THR ASP THR ASP ASN TYR ALA MET LYS SEQRES 19 B 406 SER VAL SER LYS PRO ASP SER ASP LYS LYS MET TYR GLN SEQRES 20 B 406 LEU GLU TYR ALA GLY LEU SER LYS ILE MET SER ASN LYS SEQRES 21 B 406 VAL THR ALA ALA ASN VAL PHE ASP PHE SER ARG ASP SER SEQRES 22 B 406 GLU LYS LEU ASP SER VAL MET PHE GLU THR ASP SER VAL SEQRES 23 B 406 GLY ALA LYS TYR GLU VAL TYR TYR ALA PRO VAL VAL ASN SEQRES 24 B 406 GLY VAL PRO GLN ASN ASN SER MET THR LYS LEU ALA SER SEQRES 25 B 406 GLY THR VAL SER TYR SER GLY TYR ILE ASN VAL PRO THR SEQRES 26 B 406 ASN SER TYR SER LEU PRO LYS GLY LYS GLY ALA ILE VAL SEQRES 27 B 406 VAL VAL ILE ASP ASN THR ALA ASN PRO ASN ARG GLU LYS SEQRES 28 B 406 SER THR LEU ALA TYR GLU THR ASP ILE ASP GLY TYR TYR SEQRES 29 B 406 LEU TYR GLU ALA LYS ALA ASN LEU GLY GLU SER TYR ILE SEQRES 30 B 406 LEU GLN ASN ASN LYS PHE GLU ASP ILE ASN THR TYR SER SEQRES 31 B 406 GLU PHE SER PRO CYS ASN PHE VAL ILE LYS ALA ILE THR SEQRES 32 B 406 LYS THR SER HET CA A1498 1 HET JEF A1499 8 HET CA B1498 1 HET JEF B1499 8 HETNAM CA CALCIUM ION HETNAM JEF O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE HETNAM 2 JEF GLYCOL 500) HETSYN JEF JEFFAMINE FORMUL 3 CA 2(CA 2+) FORMUL 4 JEF 2(C30 H63 N O10) FORMUL 7 HOH *449(H2 O) HELIX 1 1 ASN A 97 GLY A 102 5 6 HELIX 2 2 THR A 115 GLY A 133 1 19 HELIX 3 3 SER A 140 ALA A 148 1 9 HELIX 4 4 ASN A 165 ALA A 174 1 10 HELIX 5 5 ASP A 219 GLY A 231 1 13 HELIX 6 6 TYR A 240 TYR A 243 5 4 HELIX 7 7 SER A 274 PHE A 278 5 5 HELIX 8 8 ALA A 279 LYS A 283 5 5 HELIX 9 9 ASN A 395 MET A 398 5 4 HELIX 10 10 ASN A 478 TYR A 480 5 3 HELIX 11 11 THR B 115 GLY B 133 1 19 HELIX 12 12 SER B 140 ALA B 148 1 9 HELIX 13 13 ASN B 165 THR B 173 1 9 HELIX 14 14 ASP B 219 GLY B 231 1 13 HELIX 15 15 TYR B 240 TYR B 243 5 4 HELIX 16 16 SER B 274 PHE B 278 5 5 HELIX 17 17 ALA B 279 LYS B 283 5 5 HELIX 18 18 ASN B 395 MET B 398 5 4 HELIX 19 19 ASN B 478 TYR B 480 5 3 SHEET 1 AA 2 ALA A 95 TYR A 96 0 SHEET 2 AA 2 HIS A 262 ASP A 270 1 O TRP A 269 N TYR A 96 SHEET 1 AB 2 VAL A 233 TYR A 237 0 SHEET 2 AB 2 HIS A 262 ASP A 270 -1 O HIS A 262 N TYR A 237 SHEET 1 AC 5 ALA A 250 TYR A 251 0 SHEET 2 AC 5 PHE A 305 SER A 309 1 O TRP A 307 N TYR A 251 SHEET 3 AC 5 ALA A 289 LYS A 293 -1 O TRP A 290 N ILE A 308 SHEET 4 AC 5 HIS A 262 ASP A 270 -1 O ALA A 265 N LYS A 293 SHEET 5 AC 5 VAL A 233 TYR A 237 -1 O VAL A 233 N ILE A 266 SHEET 1 AD 5 ALA A 250 TYR A 251 0 SHEET 2 AD 5 PHE A 305 SER A 309 1 O TRP A 307 N TYR A 251 SHEET 3 AD 5 ALA A 289 LYS A 293 -1 O TRP A 290 N ILE A 308 SHEET 4 AD 5 HIS A 262 ASP A 270 -1 O ALA A 265 N LYS A 293 SHEET 5 AD 5 ALA A 95 TYR A 96 1 O TYR A 96 N TRP A 269 SHEET 1 AE 6 TYR A 322 SER A 328 0 SHEET 2 AE 6 ASN A 209 ARG A 215 -1 O ASN A 209 N SER A 328 SHEET 3 AE 6 GLY A 410 SER A 420 -1 O TYR A 411 N VAL A 213 SHEET 4 AE 6 GLU A 365 THR A 374 -1 O LEU A 367 N TYR A 419 SHEET 5 AE 6 ILE A 490 THR A 496 -1 O LYS A 491 N MET A 371 SHEET 6 AE 6 LYS A 335 TYR A 337 -1 O LYS A 335 N THR A 494 SHEET 1 AF 3 SER A 345 SER A 349 0 SHEET 2 AF 3 SER A 443 GLU A 448 -1 O SER A 443 N SER A 349 SHEET 3 AF 3 ASN A 487 PHE A 488 -1 O ASN A 487 N GLU A 448 SHEET 1 AG 2 VAL A 392 PRO A 393 0 SHEET 2 AG 2 LYS A 380 VAL A 389 -1 O VAL A 389 N VAL A 392 SHEET 1 AH 2 THR A 399 THR A 405 0 SHEET 2 AH 2 LYS A 380 VAL A 389 -1 O TYR A 381 N GLY A 404 SHEET 1 AI 6 PHE A 474 ASP A 476 0 SHEET 2 AI 6 SER A 466 LEU A 469 -1 O ILE A 468 N GLU A 475 SHEET 3 AI 6 LYS A 351 PHE A 360 -1 O THR A 353 N LEU A 469 SHEET 4 AI 6 GLY A 424 ASP A 433 -1 O GLY A 424 N PHE A 360 SHEET 5 AI 6 LYS A 380 VAL A 389 -1 O LYS A 380 N ASP A 433 SHEET 6 AI 6 VAL A 392 PRO A 393 -1 O VAL A 392 N VAL A 389 SHEET 1 AJ 6 PHE A 474 ASP A 476 0 SHEET 2 AJ 6 SER A 466 LEU A 469 -1 O ILE A 468 N GLU A 475 SHEET 3 AJ 6 LYS A 351 PHE A 360 -1 O THR A 353 N LEU A 469 SHEET 4 AJ 6 GLY A 424 ASP A 433 -1 O GLY A 424 N PHE A 360 SHEET 5 AJ 6 LYS A 380 VAL A 389 -1 O LYS A 380 N ASP A 433 SHEET 6 AJ 6 THR A 399 THR A 405 -1 O THR A 399 N TYR A 385 SHEET 1 BA 2 ALA B 95 TYR B 96 0 SHEET 2 BA 2 HIS B 262 ASP B 270 1 O TRP B 269 N TYR B 96 SHEET 1 BB 2 VAL B 233 TYR B 237 0 SHEET 2 BB 2 HIS B 262 ASP B 270 -1 O HIS B 262 N TYR B 237 SHEET 1 BC 5 ALA B 250 TYR B 251 0 SHEET 2 BC 5 PHE B 305 SER B 309 1 O TRP B 307 N TYR B 251 SHEET 3 BC 5 ALA B 289 LYS B 293 -1 O TRP B 290 N ILE B 308 SHEET 4 BC 5 HIS B 262 ASP B 270 -1 O ALA B 265 N LYS B 293 SHEET 5 BC 5 VAL B 233 TYR B 237 -1 O VAL B 233 N ILE B 266 SHEET 1 BD 5 ALA B 250 TYR B 251 0 SHEET 2 BD 5 PHE B 305 SER B 309 1 O TRP B 307 N TYR B 251 SHEET 3 BD 5 ALA B 289 LYS B 293 -1 O TRP B 290 N ILE B 308 SHEET 4 BD 5 HIS B 262 ASP B 270 -1 O ALA B 265 N LYS B 293 SHEET 5 BD 5 ALA B 95 TYR B 96 1 O TYR B 96 N TRP B 269 SHEET 1 BE 6 TYR B 322 SER B 328 0 SHEET 2 BE 6 ASN B 209 ARG B 215 -1 O ASN B 209 N SER B 328 SHEET 3 BE 6 GLY B 410 SER B 420 -1 O TYR B 411 N VAL B 213 SHEET 4 BE 6 GLU B 365 THR B 374 -1 O LEU B 367 N TYR B 419 SHEET 5 BE 6 ILE B 490 THR B 496 -1 O LYS B 491 N MET B 371 SHEET 6 BE 6 LYS B 335 TYR B 337 -1 O LYS B 335 N THR B 494 SHEET 1 BF 3 SER B 345 SER B 349 0 SHEET 2 BF 3 SER B 443 GLU B 448 -1 O SER B 443 N SER B 349 SHEET 3 BF 3 ASN B 487 PHE B 488 -1 O ASN B 487 N GLU B 448 SHEET 1 BG 6 THR B 399 THR B 405 0 SHEET 2 BG 6 LYS B 380 ALA B 386 -1 O TYR B 381 N GLY B 404 SHEET 3 BG 6 GLY B 424 ASP B 433 -1 O ALA B 427 N ALA B 386 SHEET 4 BG 6 LYS B 351 PHE B 360 -1 O VAL B 352 N ILE B 432 SHEET 5 BG 6 SER B 466 GLN B 470 -1 O TYR B 467 N ALA B 355 SHEET 6 BG 6 LYS B 473 ASP B 476 -1 O LYS B 473 N GLN B 470 SHEET 1 BH 2 VAL B 388 VAL B 389 0 SHEET 2 BH 2 VAL B 392 PRO B 393 -1 O VAL B 392 N VAL B 389 LINK O LEU A 339 CA CA A1498 1555 1555 2.33 LINK OE1 GLU A 448 CA CA A1498 1555 1555 2.52 LINK O LYS A 460 CA CA A1498 1555 1555 2.17 LINK OD1 ASN A 487 CA CA A1498 1555 1555 2.29 LINK CA CA A1498 O JEF A1499 1555 1555 2.45 LINK CA CA A1498 O10 JEF A1499 1555 1555 2.57 LINK CA CA A1498 O11 JEF A1499 1555 1555 2.71 LINK O LEU B 339 CA CA B1498 1555 1555 2.29 LINK OE1 GLU B 448 CA CA B1498 1555 1555 2.54 LINK O LYS B 460 CA CA B1498 1555 1555 2.37 LINK OD1 ASN B 487 CA CA B1498 1555 1555 2.24 LINK CA CA B1498 O11 JEF B1499 1555 1555 2.96 LINK CA CA B1498 O10 JEF B1499 1555 1555 2.69 LINK CA CA B1498 O JEF B1499 1555 1555 2.73 CISPEP 1 GLY A 177 PRO A 178 0 11.81 CISPEP 2 SER A 484 PRO A 485 0 5.80 CISPEP 3 SER A 484 PRO A 485 0 5.16 CISPEP 4 GLY B 177 PRO B 178 0 8.09 CISPEP 5 SER B 484 PRO B 485 0 -8.53 SITE 1 AC1 5 LEU A 339 GLU A 448 LYS A 460 ASN A 487 SITE 2 AC1 5 JEF A1499 SITE 1 AC2 5 LEU B 339 GLU B 448 LYS B 460 ASN B 487 SITE 2 AC2 5 JEF B1499 SITE 1 AC3 6 LEU A 339 GLU A 448 LYS A 460 GLU A 465 SITE 2 AC3 6 ASN A 487 CA A1498 SITE 1 AC4 6 LEU B 339 GLU B 448 LYS B 460 GLU B 465 SITE 2 AC4 6 ASN B 487 CA B1498 CRYST1 42.220 58.421 93.100 89.28 77.96 71.62 P 1 2 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 0.023685 -0.007870 -0.005512 0.00000 SCALE2 0.000000 0.018037 0.001036 0.00000 SCALE3 0.000000 0.000000 0.011001 0.00000