HEADER HYDROLASE 07-NOV-09 3KLC TITLE CRYSTAL STRUCTURE OF HYPERTHERMOPHILIC NITRILASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA UREIDOPROPIONASE (BETA-ALANINE SYNTHASE); COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.1.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 STRAIN: GE5; SOURCE 5 GENE: NIT-30, PAB1449, PYRAB13990; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS ALPHA-BETA SANDWICH, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.RACZYNSKA,C.VORGIAS,G.ANTRANIKIAN,W.RYPNIEWSKI REVDAT 4 06-SEP-23 3KLC 1 REMARK LINK REVDAT 3 13-JUL-11 3KLC 1 VERSN REVDAT 2 02-FEB-11 3KLC 1 JRNL REVDAT 1 24-NOV-10 3KLC 0 JRNL AUTH J.E.RACZYNSKA,C.E.VORGIAS,G.ANTRANIKIAN,W.RYPNIEWSKI JRNL TITL CRYSTALLOGRAPHIC ANALYSIS OF A THERMOACTIVE NITRILASE. JRNL REF J.STRUCT.BIOL. V. 173 294 2010 JRNL REFN ISSN 1047-8477 JRNL PMID 21095228 JRNL DOI 10.1016/J.JSB.2010.11.017 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.9 REMARK 3 NUMBER OF REFLECTIONS : 35951 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1940 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 958 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 30.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.5920 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.4430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4178 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -22.21000 REMARK 3 B22 (A**2) : -22.21000 REMARK 3 B33 (A**2) : 44.43000 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): 0.031 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.027 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.592 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4288 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5784 ; 1.793 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 522 ; 7.210 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;36.635 ;23.816 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 757 ;15.890 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;19.060 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 631 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3264 ; 0.009 ; 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): 2609 ; 0.943 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4206 ; 1.547 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1679 ; 2.718 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1575 ; 4.103 ; 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.581 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H, K, -L REMARK 3 TWIN FRACTION : 0.419 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 3KLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91163, 0.91994, 0.88557 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37990 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 30.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43100 REMARK 200 R SYM FOR SHELL (I) : 0.43100 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3KI8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 33% PEG 550MME, 0.2M MG(CH3COOH)2 AND REMARK 280 0.2 TRISHCL. THE CRYSTAL SOAKED WITH 1M KBR FOR ~1 MINUTE, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 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 64.59800 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 32.29900 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 96.89700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 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 465 MET B 1 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 ILE B 145 C CSX B 146 N 0.217 REMARK 500 CSX B 146 C PHE B 147 N 0.205 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 TYR A 118 -126.06 60.74 REMARK 500 CSX A 146 -111.11 39.09 REMARK 500 TYR B 118 -125.24 50.05 REMARK 500 CSX B 146 -110.23 37.39 REMARK 500 ARG B 256 79.57 -119.31 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 MG B 270 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 255 O REMARK 620 2 GLU B 257 OE2 77.9 REMARK 620 3 HOH B 286 O 84.3 84.5 REMARK 620 4 HOH B 296 O 158.6 85.0 81.2 REMARK 620 5 HOH B 340 O 92.4 165.8 84.3 101.7 REMARK 620 6 HOH B 359 O 104.8 88.8 167.3 87.5 103.8 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 BR A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 268 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 269 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 270 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IVZ RELATED DB: PDB REMARK 900 UNLIGANDED NITRILASE - TETRAGONAL FORM REMARK 900 RELATED ID: 3IW3 RELATED DB: PDB REMARK 900 NITRILASE WITH ACETATE ION - TETRAGONAL FORM REMARK 900 RELATED ID: 3KI8 RELATED DB: PDB REMARK 900 NITRILASE WITH ACETATE ION - MONOCLINIC FORM REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHORS RESIDUE AT POSITION 238 IS MORE LIKELY A REMARK 999 SER. DBREF 3KLC A 1 262 UNP Q9UYV8 Q9UYV8_PYRAB 1 262 DBREF 3KLC B 1 262 UNP Q9UYV8 Q9UYV8_PYRAB 1 262 SEQADV 3KLC SER A 238 UNP Q9UYV8 TYR 238 SEE REMARK 999 SEQADV 3KLC SER B 238 UNP Q9UYV8 TYR 238 SEE REMARK 999 SEQRES 1 A 262 MET VAL LYS VAL ALA TYR VAL GLN MET ASN PRO GLN ILE SEQRES 2 A 262 LEU GLU PRO ASP LYS ASN TYR SER LYS ALA GLU LYS LEU SEQRES 3 A 262 ILE LYS GLU ALA SER LYS GLN GLY ALA GLN LEU VAL VAL SEQRES 4 A 262 LEU PRO GLU LEU PHE ASP THR GLY TYR ASN PHE GLU THR SEQRES 5 A 262 ARG GLU GLU VAL PHE GLU ILE ALA GLN LYS ILE PRO GLU SEQRES 6 A 262 GLY GLU THR THR THR PHE LEU MET ASP VAL ALA ARG ASP SEQRES 7 A 262 THR GLY VAL TYR ILE VAL ALA GLY THR ALA GLU LYS ASP SEQRES 8 A 262 GLY ASP VAL LEU TYR ASN SER ALA VAL VAL VAL GLY PRO SEQRES 9 A 262 ARG GLY PHE ILE GLY LYS TYR ARG LYS ILE HIS LEU PHE SEQRES 10 A 262 TYR ARG GLU LYS PHE PHE PHE GLU PRO GLY ASP LEU GLY SEQRES 11 A 262 PHE ARG VAL PHE ASP LEU GLY PHE MET LYS VAL GLY VAL SEQRES 12 A 262 MET ILE CSX PHE ASP TRP PHE PHE PRO GLU SER ALA ARG SEQRES 13 A 262 THR LEU ALA LEU LYS GLY ALA ASP VAL ILE ALA HIS PRO SEQRES 14 A 262 ALA ASN LEU VAL MET PRO TYR ALA PRO ARG ALA MET PRO SEQRES 15 A 262 ILE ARG ALA LEU GLU ASN LYS VAL TYR THR VAL THR ALA SEQRES 16 A 262 ASP ARG VAL GLY GLU GLU ARG GLY LEU LYS PHE ILE GLY SEQRES 17 A 262 LYS SER LEU ILE ALA SER PRO LYS ALA GLU VAL LEU SER SEQRES 18 A 262 MET ALA SER GLU THR GLU GLU GLU VAL GLY VAL ALA GLU SEQRES 19 A 262 ILE ASP LEU SER LEU VAL ARG ASN LYS ARG ILE ASN ASP SEQRES 20 A 262 LEU ASN ASP ILE PHE LYS ASP ARG ARG GLU GLU TYR TYR SEQRES 21 A 262 PHE ARG SEQRES 1 B 262 MET VAL LYS VAL ALA TYR VAL GLN MET ASN PRO GLN ILE SEQRES 2 B 262 LEU GLU PRO ASP LYS ASN TYR SER LYS ALA GLU LYS LEU SEQRES 3 B 262 ILE LYS GLU ALA SER LYS GLN GLY ALA GLN LEU VAL VAL SEQRES 4 B 262 LEU PRO GLU LEU PHE ASP THR GLY TYR ASN PHE GLU THR SEQRES 5 B 262 ARG GLU GLU VAL PHE GLU ILE ALA GLN LYS ILE PRO GLU SEQRES 6 B 262 GLY GLU THR THR THR PHE LEU MET ASP VAL ALA ARG ASP SEQRES 7 B 262 THR GLY VAL TYR ILE VAL ALA GLY THR ALA GLU LYS ASP SEQRES 8 B 262 GLY ASP VAL LEU TYR ASN SER ALA VAL VAL VAL GLY PRO SEQRES 9 B 262 ARG GLY PHE ILE GLY LYS TYR ARG LYS ILE HIS LEU PHE SEQRES 10 B 262 TYR ARG GLU LYS PHE PHE PHE GLU PRO GLY ASP LEU GLY SEQRES 11 B 262 PHE ARG VAL PHE ASP LEU GLY PHE MET LYS VAL GLY VAL SEQRES 12 B 262 MET ILE CSX PHE ASP TRP PHE PHE PRO GLU SER ALA ARG SEQRES 13 B 262 THR LEU ALA LEU LYS GLY ALA ASP VAL ILE ALA HIS PRO SEQRES 14 B 262 ALA ASN LEU VAL MET PRO TYR ALA PRO ARG ALA MET PRO SEQRES 15 B 262 ILE ARG ALA LEU GLU ASN LYS VAL TYR THR VAL THR ALA SEQRES 16 B 262 ASP ARG VAL GLY GLU GLU ARG GLY LEU LYS PHE ILE GLY SEQRES 17 B 262 LYS SER LEU ILE ALA SER PRO LYS ALA GLU VAL LEU SER SEQRES 18 B 262 MET ALA SER GLU THR GLU GLU GLU VAL GLY VAL ALA GLU SEQRES 19 B 262 ILE ASP LEU SER LEU VAL ARG ASN LYS ARG ILE ASN ASP SEQRES 20 B 262 LEU ASN ASP ILE PHE LYS ASP ARG ARG GLU GLU TYR TYR SEQRES 21 B 262 PHE ARG MODRES 3KLC CSX A 146 CYS S-OXY CYSTEINE MODRES 3KLC CSX B 146 CYS S-OXY CYSTEINE HET CSX A 146 7 HET CSX B 146 7 HET BR A 263 1 HET BR A 264 2 HET BR A 265 1 HET BR A 266 1 HET BR A 267 1 HET BR A 268 1 HET ACY A 269 4 HET BR A 270 1 HET BR B 263 1 HET BR B 264 1 HET BR B 265 1 HET BR B 266 1 HET BR B 267 1 HET ACY B 268 4 HET BR B 269 1 HET MG B 270 1 HETNAM CSX S-OXY CYSTEINE HETNAM BR BROMIDE ION HETNAM ACY ACETIC ACID HETNAM MG MAGNESIUM ION FORMUL 1 CSX 2(C3 H7 N O3 S) FORMUL 3 BR 13(BR 1-) FORMUL 9 ACY 2(C2 H4 O2) FORMUL 18 MG MG 2+ FORMUL 19 HOH *218(H2 O) HELIX 1 1 GLU A 15 GLN A 33 1 19 HELIX 2 2 THR A 52 GLU A 58 1 7 HELIX 3 3 GLY A 66 GLY A 80 1 15 HELIX 4 4 ARG A 119 PHE A 124 1 6 HELIX 5 5 ILE A 145 PHE A 150 5 6 HELIX 6 6 PHE A 151 LYS A 161 1 11 HELIX 7 7 TYR A 176 LYS A 189 1 14 HELIX 8 8 ASP A 236 ASN A 242 1 7 HELIX 9 9 ILE A 251 ARG A 255 1 5 HELIX 10 10 ARG A 256 TYR A 260 5 5 HELIX 11 11 GLU B 15 GLN B 33 1 19 HELIX 12 12 THR B 52 ALA B 60 1 9 HELIX 13 13 GLY B 66 GLY B 80 1 15 HELIX 14 14 ARG B 119 PHE B 124 1 6 HELIX 15 15 ILE B 145 PHE B 150 5 6 HELIX 16 16 PHE B 151 LYS B 161 1 11 HELIX 17 17 TYR B 176 LYS B 189 1 14 HELIX 18 18 ASP B 236 ASN B 242 1 7 HELIX 19 19 ASP B 250 ARG B 255 1 6 HELIX 20 20 ARG B 256 TYR B 260 5 5 SHEET 1 A 6 GLY A 106 ARG A 112 0 SHEET 2 A 6 VAL A 94 GLY A 103 -1 N VAL A 101 O GLY A 109 SHEET 3 A 6 TYR A 82 ASP A 91 -1 N ASP A 91 O VAL A 94 SHEET 4 A 6 LEU A 37 VAL A 39 1 N VAL A 38 O VAL A 84 SHEET 5 A 6 LYS A 3 GLN A 8 1 N VAL A 7 O VAL A 39 SHEET 6 A 6 GLU A 229 GLU A 234 -1 O GLU A 229 N GLN A 8 SHEET 1 B 6 VAL A 133 ASP A 135 0 SHEET 2 B 6 LYS A 140 VAL A 143 -1 O VAL A 141 N PHE A 134 SHEET 3 B 6 VAL A 165 ALA A 170 1 O ALA A 167 N GLY A 142 SHEET 4 B 6 TYR A 191 ASP A 196 1 O VAL A 193 N HIS A 168 SHEET 5 B 6 LEU A 211 ALA A 213 -1 O LEU A 211 N THR A 194 SHEET 6 B 6 VAL A 219 MET A 222 -1 O SER A 221 N ILE A 212 SHEET 1 C 2 GLU A 200 GLU A 201 0 SHEET 2 C 2 LEU A 204 LYS A 205 -1 O LEU A 204 N GLU A 201 SHEET 1 D 2 ARG A 244 ASN A 246 0 SHEET 2 D 2 ASN A 249 ASP A 250 -1 O ASN A 249 N ILE A 245 SHEET 1 E 4 GLN B 61 LYS B 62 0 SHEET 2 E 4 TYR B 82 ASP B 91 1 O LYS B 90 N GLN B 61 SHEET 3 E 4 VAL B 94 GLY B 103 -1 O VAL B 102 N ILE B 83 SHEET 4 E 4 GLY B 106 ARG B 112 -1 O GLY B 109 N VAL B 101 SHEET 1 F 5 GLN B 61 LYS B 62 0 SHEET 2 F 5 TYR B 82 ASP B 91 1 O LYS B 90 N GLN B 61 SHEET 3 F 5 ALA B 35 VAL B 39 1 N VAL B 38 O TYR B 82 SHEET 4 F 5 LYS B 3 GLN B 8 1 N VAL B 7 O VAL B 39 SHEET 5 F 5 GLU B 229 GLU B 234 -1 O GLU B 229 N GLN B 8 SHEET 1 G 6 VAL B 133 ASP B 135 0 SHEET 2 G 6 LYS B 140 VAL B 143 -1 O VAL B 141 N PHE B 134 SHEET 3 G 6 VAL B 165 ALA B 170 1 O VAL B 165 N GLY B 142 SHEET 4 G 6 TYR B 191 ASP B 196 1 O VAL B 193 N ILE B 166 SHEET 5 G 6 LEU B 211 ALA B 213 -1 O LEU B 211 N THR B 194 SHEET 6 G 6 VAL B 219 MET B 222 -1 O LEU B 220 N ILE B 212 SHEET 1 H 2 GLU B 200 GLU B 201 0 SHEET 2 H 2 LEU B 204 LYS B 205 -1 O LEU B 204 N GLU B 201 LINK C ILE A 145 N CSX A 146 1555 1555 1.39 LINK C CSX A 146 N PHE A 147 1555 1555 1.44 LINK C ILE B 145 N CSX B 146 1555 1555 1.55 LINK C CSX B 146 N PHE B 147 1555 1555 1.54 LINK O ARG B 255 MG MG B 270 1555 1555 2.03 LINK OE2 GLU B 257 MG MG B 270 1555 1555 2.27 LINK MG MG B 270 O HOH B 286 1555 1555 2.14 LINK MG MG B 270 O HOH B 296 1555 1555 2.15 LINK MG MG B 270 O HOH B 340 1555 1555 2.08 LINK MG MG B 270 O HOH B 359 1555 1555 2.02 CISPEP 1 ILE A 63 PRO A 64 0 5.17 CISPEP 2 ILE B 63 PRO B 64 0 5.73 SITE 1 AC1 4 PHE A 107 GLY A 109 LYS A 110 ARG A 132 SITE 1 AC2 4 GLU A 15 PRO A 16 ASP A 17 LYS A 18 SITE 1 AC3 2 GLY A 103 ARG A 105 SITE 1 AC4 3 LYS A 3 GLY A 34 GLY B 34 SITE 1 AC5 2 ARG A 132 VAL A 133 SITE 1 AC6 3 GLU A 153 GLU B 153 PHE B 261 SITE 1 AC7 8 CSX A 146 TRP A 149 LEU A 172 VAL A 173 SITE 2 AC7 8 MET A 174 BR A 270 HOH A 306 HOH A 322 SITE 1 AC8 5 TRP A 149 LEU A 172 ACY A 269 HOH A 306 SITE 2 AC8 5 HOH A 322 SITE 1 AC9 3 GLY B 103 PRO B 104 ARG B 105 SITE 1 BC1 2 LYS B 110 ARG B 132 SITE 1 BC2 1 LYS B 22 SITE 1 BC3 1 PRO B 175 SITE 1 BC4 2 ALA B 233 GLU B 234 SITE 1 BC5 7 TRP B 149 LEU B 172 VAL B 173 MET B 174 SITE 2 BC5 7 BR B 269 HOH B 307 HOH B 341 SITE 1 BC6 3 TRP B 149 LEU B 172 ACY B 268 SITE 1 BC7 6 ARG B 255 GLU B 257 HOH B 286 HOH B 296 SITE 2 BC7 6 HOH B 340 HOH B 359 CRYST1 59.283 59.283 129.196 90.00 90.00 90.00 P 41 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 0.016868 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007740 0.00000