HEADER HYDROLASE 02-SEP-09 3IW3 TITLE CRYSTAL STRUCTURE OF HYPERTHERMOPHILIC NITRILASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRILASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BETA UREIDOPROPIONASE, BETA-ALANINE SYNTHASE; COMPND 5 EC: 3.5.1.6; COMPND 6 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 3IW3 1 REMARK LINK REVDAT 3 19-NOV-14 3IW3 1 HET HETATM HETNAM HETSYN REVDAT 3 2 1 VERSN REVDAT 2 02-FEB-11 3IW3 1 JRNL REVDAT 1 22-SEP-10 3IW3 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0092 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 38574 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2057 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2672 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4180 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 274 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.04000 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): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.896 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4369 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5908 ; 1.649 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 541 ; 6.646 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 209 ;35.840 ;23.780 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 773 ;15.241 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;18.459 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 648 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3330 ; 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): 2654 ; 0.877 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4288 ; 1.488 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1715 ; 2.723 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1610 ; 4.372 ; 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 : 1.20 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 3IW3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000054937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-07 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) : 0.92918 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40685 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : 0.09500 REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.48300 REMARK 200 R SYM FOR SHELL (I) : 0.48300 REMARK 200 FOR SHELL : 3.200 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: 3IVZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 550MME, 0.2M MGCL2 OR REMARK 280 MG(CH3COOH)2 AND 0.2M TRISHCL PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 64.48750 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 32.24375 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 96.73125 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: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 CSD B 146 N 0.223 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 CSD A 146 O - C - N ANGL. DEV. = -9.7 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 TYR A 118 -126.38 58.65 REMARK 500 CSD A 146 -116.72 54.47 REMARK 500 TYR B 118 -121.67 40.90 REMARK 500 CSD B 146 -127.70 54.90 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 A 264 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 222 O REMARK 620 2 HOH A 269 O 81.4 REMARK 620 3 HOH A 445 O 142.4 118.6 REMARK 620 4 HOH A 446 O 73.5 87.7 75.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 1432 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 264 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IVZ RELATED DB: PDB REMARK 900 UNLIGANDED NITRILASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHORS RESIDUE AT POSITION 238 IS MORE LIKELY A REMARK 999 SER. DBREF 3IW3 A 1 262 UNP Q9UYV8 Q9UYV8_PYRAB 1 262 DBREF 3IW3 B 1 262 UNP Q9UYV8 Q9UYV8_PYRAB 1 262 SEQADV 3IW3 SER A 238 UNP Q9UYV8 TYR 238 SEE REMARK 999 SEQADV 3IW3 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 CSD 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 CSD 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 3IW3 CSD A 146 CYS 3-SULFINOALANINE MODRES 3IW3 CSD B 146 CYS 3-SULFINOALANINE HET CSD A 146 8 HET CSD B 146 8 HET ACY A 263 4 HET ACY A1432 4 HET MG A 264 1 HET ACY B 263 4 HETNAM CSD 3-SULFINOALANINE HETNAM ACY ACETIC ACID HETNAM MG MAGNESIUM ION HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD 2(C3 H7 N O4 S) FORMUL 3 ACY 3(C2 H4 O2) FORMUL 5 MG MG 2+ FORMUL 7 HOH *274(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 PHE A 117 PHE A 123 5 7 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 GLU B 58 1 7 HELIX 13 13 GLY B 66 GLY B 80 1 15 HELIX 14 14 PHE B 117 PHE B 123 5 7 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 ILE B 251 ARG B 255 1 5 HELIX 20 20 ARG B 256 TYR B 260 5 5 SHEET 1 A 4 GLN A 61 LYS A 62 0 SHEET 2 A 4 TYR A 82 ASP A 91 1 O LYS A 90 N GLN A 61 SHEET 3 A 4 VAL A 94 GLY A 103 -1 O TYR A 96 N GLU A 89 SHEET 4 A 4 GLY A 106 ARG A 112 -1 O GLY A 109 N VAL A 101 SHEET 1 B 5 GLN A 61 LYS A 62 0 SHEET 2 B 5 TYR A 82 ASP A 91 1 O LYS A 90 N GLN A 61 SHEET 3 B 5 LEU A 37 VAL A 39 1 N VAL A 38 O TYR A 82 SHEET 4 B 5 LYS A 3 GLN A 8 1 N ALA A 5 O VAL A 39 SHEET 5 B 5 GLU A 229 GLU A 234 -1 O GLU A 229 N GLN A 8 SHEET 1 C 6 VAL A 133 ASP A 135 0 SHEET 2 C 6 LYS A 140 VAL A 143 -1 O VAL A 141 N PHE A 134 SHEET 3 C 6 VAL A 165 PRO A 169 1 O ALA A 167 N GLY A 142 SHEET 4 C 6 TYR A 191 ALA A 195 1 O VAL A 193 N HIS A 168 SHEET 5 C 6 LEU A 211 ALA A 213 -1 O LEU A 211 N THR A 194 SHEET 6 C 6 VAL A 219 MET A 222 -1 O LEU A 220 N ILE A 212 SHEET 1 D 2 GLU A 200 GLU A 201 0 SHEET 2 D 2 LEU A 204 LYS A 205 -1 O LEU A 204 N GLU A 201 SHEET 1 E 2 ARG A 244 ASN A 246 0 SHEET 2 E 2 ASN A 249 ASP A 250 -1 O ASN A 249 N ILE A 245 SHEET 1 F 6 GLY B 106 ARG B 112 0 SHEET 2 F 6 VAL B 94 GLY B 103 -1 N VAL B 101 O GLY B 109 SHEET 3 F 6 TYR B 82 ASP B 91 -1 N GLU B 89 O TYR B 96 SHEET 4 F 6 LEU B 37 VAL B 39 1 N VAL B 38 O TYR B 82 SHEET 5 F 6 LYS B 3 GLN B 8 1 N VAL B 7 O VAL B 39 SHEET 6 F 6 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 ALA B 167 N GLY B 142 SHEET 4 G 6 TYR B 191 ASP B 196 1 O VAL B 193 N HIS B 168 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 SHEET 1 I 2 ARG B 244 ASN B 246 0 SHEET 2 I 2 ASN B 249 ASP B 250 -1 O ASN B 249 N ILE B 245 LINK C ILE A 145 N CSD A 146 1555 1555 1.44 LINK C CSD A 146 N PHE A 147 1555 1555 1.47 LINK C ILE B 145 N CSD B 146 1555 1555 1.56 LINK C CSD B 146 N PHE B 147 1555 1555 1.41 LINK O MET A 222 MG MG A 264 1555 1555 2.55 LINK MG MG A 264 O HOH A 269 1555 1555 2.22 LINK MG MG A 264 O HOH A 445 1555 1555 2.10 LINK MG MG A 264 O HOH A 446 1555 1555 2.20 CISPEP 1 ILE A 63 PRO A 64 0 2.75 CISPEP 2 ILE B 63 PRO B 64 0 3.47 SITE 1 AC1 6 CSD A 146 TRP A 149 LEU A 172 VAL A 173 SITE 2 AC1 6 MET A 174 HOH A 320 SITE 1 AC2 6 CSD B 146 TRP B 149 LEU B 172 VAL B 173 SITE 2 AC2 6 MET B 174 HOH B 264 SITE 1 AC3 6 TYR A 82 ARG A 105 LEU A 136 HOH A 274 SITE 2 AC3 6 HOH A 371 GLY B 137 SITE 1 AC4 4 MET A 222 HOH A 269 HOH A 445 HOH A 446 CRYST1 59.162 59.162 128.975 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 0.016938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007791 0.00000