HEADER LYASE 25-SEP-12 3VYH TITLE CRYSTAL STRUCTURE OF AW116R MUTANT OF NITRILE HYDRATASE FROM TITLE 2 PSEUDONOCARDIA THERMOPHILLA COMPND MOL_ID: 1; COMPND 2 MOLECULE: COBALT-CONTAINING NITRILE HYDRATASE SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-NHASE, L-NITRILASE; COMPND 5 EC: 4.2.1.84; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: COBALT-CONTAINING NITRILE HYDRATASE SUBUNIT BETA; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: L-NHASE, L-NITRILASE; COMPND 12 EC: 4.2.1.84; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDONOCARDIA THERMOPHILA; SOURCE 3 ORGANISM_TAXID: 1848; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: PSEUDONOCARDIA THERMOPHILA; SOURCE 8 ORGANISM_TAXID: 1848; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NITRILE HYDRATASE, METALLOENZYME, HYDRATION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.YAMANAKA,M.SATO,T.ARAKAWA,S.NAMIMA,S.HORI,A.OHTAKI,K.NOGUCHI, AUTHOR 2 Y.KATAYAMA,M.YOHDA,M.ODAKA REVDAT 3 06-DEC-23 3VYH 1 REMARK REVDAT 2 08-NOV-23 3VYH 1 REMARK SEQADV LINK REVDAT 1 13-NOV-13 3VYH 0 JRNL AUTH Y.YAMANAKA,M.SATO,T.ARAKAWA,S.NAMIMA,S.HORI,A.OHTAKI, JRNL AUTH 2 K.NOGUCHI,Y.KATAYAMA,M.YOHDA,M.ODAKA JRNL TITL EFFECTS OF ARGNINE RESIDUE AROUND THE SUBSTRATE POCKET ON JRNL TITL 2 THE SUBSTRATE SPECIFICITY OF THIOCYANATE HYDROLASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.63 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 55668 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2962 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) : 1.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4062 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 212 REMARK 3 BIN FREE R VALUE : 0.2200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3449 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 368 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.088 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.471 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3534 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4798 ; 2.202 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ;11.303 ; 5.047 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;34.687 ;23.584 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 580 ;12.658 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.226 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 499 ; 0.174 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2758 ; 0.014 ; 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): 2139 ; 1.307 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3462 ; 2.055 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1395 ; 3.162 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1336 ; 4.923 ; 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 3VYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000095658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61652 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1IRE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NAOH PH7.5, 1.4M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 123.19733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.59867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.59867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 123.19733 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -107.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 61.59867 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 ASP B 227 REMARK 465 THR B 228 REMARK 465 LYS B 229 REMARK 465 ALA B 230 REMARK 465 ALA B 231 REMARK 465 ALA B 232 REMARK 465 ALA B 233 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 ASP B 134 CB CG OD1 OD2 REMARK 480 ARG B 135 CG CD NE CZ NH1 NH2 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 O HOH A 481 O HOH B 499 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 496 O HOH B 507 1455 1.86 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 ARG B 160 CG ARG B 160 CD 0.155 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 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 7 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 134 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 VAL A 204 CB - CA - C ANGL. DEV. = 11.8 DEGREES REMARK 500 LEU B 13 CB - CG - CD1 ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG B 26 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET B 46 CG - SD - CE ANGL. DEV. = -25.7 DEGREES REMARK 500 ARG B 131 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 135 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR B 222 CB - CG - CD2 ANGL. DEV. = -3.7 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 CSD A 111 -91.37 -165.81 REMARK 500 SER A 112 11.80 -168.63 REMARK 500 ARG B 157 58.72 -113.40 REMARK 500 ARG B 158 72.17 -119.18 REMARK 500 CYS B 189 57.33 36.16 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 CO A 301 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 108 SG REMARK 620 2 CSD A 111 SG 95.6 REMARK 620 3 SER A 112 N 97.0 94.9 REMARK 620 4 CSO A 113 N 96.8 167.4 85.8 REMARK 620 5 CSO A 113 SG 89.0 92.2 170.2 85.8 REMARK 620 6 HOH A 527 O 173.8 84.1 89.2 83.3 84.8 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 CO A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VYG RELATED DB: PDB DBREF 3VYH A 1 204 UNP Q7SID2 NHAA_PSETH 1 204 DBREF 3VYH B 1 233 UNP Q7SID3 NHAB_PSETH 1 233 SEQADV 3VYH ARG A 116 UNP Q7SID2 TRP 116 ENGINEERED MUTATION SEQRES 1 A 204 MET THR GLU ASN ILE LEU ARG LYS SER ASP GLU GLU ILE SEQRES 2 A 204 GLN LYS GLU ILE THR ALA ARG VAL LYS ALA LEU GLU SER SEQRES 3 A 204 MET LEU ILE GLU GLN GLY ILE LEU THR THR SER MET ILE SEQRES 4 A 204 ASP ARG MET ALA GLU ILE TYR GLU ASN GLU VAL GLY PRO SEQRES 5 A 204 HIS LEU GLY ALA LYS VAL VAL VAL LYS ALA TRP THR ASP SEQRES 6 A 204 PRO GLU PHE LYS LYS ARG LEU LEU ALA ASP GLY THR GLU SEQRES 7 A 204 ALA CYS LYS GLU LEU GLY ILE GLY GLY LEU GLN GLY GLU SEQRES 8 A 204 ASP MET MET TRP VAL GLU ASN THR ASP GLU VAL HIS HIS SEQRES 9 A 204 VAL VAL VAL CYS THR LEU CSD SER CSO TYR PRO ARG PRO SEQRES 10 A 204 VAL LEU GLY LEU PRO PRO ASN TRP PHE LYS GLU PRO GLN SEQRES 11 A 204 TYR ARG SER ARG VAL VAL ARG GLU PRO ARG GLN LEU LEU SEQRES 12 A 204 LYS GLU GLU PHE GLY PHE GLU VAL PRO PRO SER LYS GLU SEQRES 13 A 204 ILE LYS VAL TRP ASP SER SER SER GLU MET ARG PHE VAL SEQRES 14 A 204 VAL LEU PRO GLN ARG PRO ALA GLY THR ASP GLY TRP SER SEQRES 15 A 204 GLU GLU GLU LEU ALA THR LEU VAL THR ARG GLU SER MET SEQRES 16 A 204 ILE GLY VAL GLU PRO ALA LYS ALA VAL SEQRES 1 B 233 MET ASN GLY VAL TYR ASP VAL GLY GLY THR ASP GLY LEU SEQRES 2 B 233 GLY PRO ILE ASN ARG PRO ALA ASP GLU PRO VAL PHE ARG SEQRES 3 B 233 ALA GLU TRP GLU LYS VAL ALA PHE ALA MET PHE PRO ALA SEQRES 4 B 233 THR PHE ARG ALA GLY PHE MET GLY LEU ASP GLU PHE ARG SEQRES 5 B 233 PHE GLY ILE GLU GLN MET ASN PRO ALA GLU TYR LEU GLU SEQRES 6 B 233 SER PRO TYR TYR TRP HIS TRP ILE ARG THR TYR ILE HIS SEQRES 7 B 233 HIS GLY VAL ARG THR GLY LYS ILE ASP LEU GLU GLU LEU SEQRES 8 B 233 GLU ARG ARG THR GLN TYR TYR ARG GLU ASN PRO ASP ALA SEQRES 9 B 233 PRO LEU PRO GLU HIS GLU GLN LYS PRO GLU LEU ILE GLU SEQRES 10 B 233 PHE VAL ASN GLN ALA VAL TYR GLY GLY LEU PRO ALA SER SEQRES 11 B 233 ARG GLU VAL ASP ARG PRO PRO LYS PHE LYS GLU GLY ASP SEQRES 12 B 233 VAL VAL ARG PHE SER THR ALA SER PRO LYS GLY HIS ALA SEQRES 13 B 233 ARG ARG ALA ARG TYR VAL ARG GLY LYS THR GLY THR VAL SEQRES 14 B 233 VAL LYS HIS HIS GLY ALA TYR ILE TYR PRO ASP THR ALA SEQRES 15 B 233 GLY ASN GLY LEU GLY GLU CYS PRO GLU HIS LEU TYR THR SEQRES 16 B 233 VAL ARG PHE THR ALA GLN GLU LEU TRP GLY PRO GLU GLY SEQRES 17 B 233 ASP PRO ASN SER SER VAL TYR TYR ASP CYS TRP GLU PRO SEQRES 18 B 233 TYR ILE GLU LEU VAL ASP THR LYS ALA ALA ALA ALA MODRES 3VYH CSD A 111 CYS 3-SULFINOALANINE MODRES 3VYH CSO A 113 CYS S-HYDROXYCYSTEINE HET CSD A 111 8 HET CSO A 113 7 HET CO A 301 1 HETNAM CSD 3-SULFINOALANINE HETNAM CSO S-HYDROXYCYSTEINE HETNAM CO COBALT (II) ION HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD C3 H7 N O4 S FORMUL 1 CSO C3 H7 N O3 S FORMUL 3 CO CO 2+ FORMUL 4 HOH *368(H2 O) HELIX 1 1 SER A 9 GLN A 31 1 23 HELIX 2 2 THR A 35 GLU A 49 1 15 HELIX 3 3 GLY A 51 ASP A 65 1 15 HELIX 4 4 ASP A 65 ASP A 75 1 11 HELIX 5 5 ASP A 75 GLU A 82 1 8 HELIX 6 6 PRO A 115 GLY A 120 1 6 HELIX 7 7 PRO A 123 GLU A 128 1 6 HELIX 8 8 GLU A 128 VAL A 136 1 9 HELIX 9 9 GLU A 138 GLY A 148 1 11 HELIX 10 10 SER A 182 THR A 188 1 7 HELIX 11 11 THR A 191 GLY A 197 1 7 HELIX 12 12 ALA B 27 ALA B 43 1 17 HELIX 13 13 GLY B 47 GLN B 57 1 11 HELIX 14 14 ASN B 59 SER B 66 1 8 HELIX 15 15 PRO B 67 THR B 83 1 17 HELIX 16 16 ASP B 87 ASN B 101 1 15 HELIX 17 17 LYS B 112 GLY B 126 1 15 HELIX 18 18 ALA B 159 ARG B 163 5 5 HELIX 19 19 TYR B 178 GLY B 183 1 6 HELIX 20 20 ALA B 200 GLY B 205 1 6 HELIX 21 21 PRO B 206 GLY B 208 5 3 SHEET 1 A 2 MET A 93 GLU A 97 0 SHEET 2 A 2 ARG A 167 LEU A 171 1 O LEU A 171 N VAL A 96 SHEET 1 B 6 VAL A 102 VAL A 107 0 SHEET 2 B 6 GLU A 156 ASP A 161 1 O LYS A 158 N HIS A 103 SHEET 3 B 6 SER B 212 TRP B 219 1 O TYR B 215 N VAL A 159 SHEET 4 B 6 GLU B 191 THR B 199 -1 N TYR B 194 O CYS B 218 SHEET 5 B 6 THR B 166 TYR B 176 -1 N VAL B 170 O THR B 195 SHEET 6 B 6 SER B 130 ARG B 131 -1 N ARG B 131 O ALA B 175 SHEET 1 C 7 VAL A 102 VAL A 107 0 SHEET 2 C 7 GLU A 156 ASP A 161 1 O LYS A 158 N HIS A 103 SHEET 3 C 7 SER B 212 TRP B 219 1 O TYR B 215 N VAL A 159 SHEET 4 C 7 GLU B 191 THR B 199 -1 N TYR B 194 O CYS B 218 SHEET 5 C 7 THR B 166 TYR B 176 -1 N VAL B 170 O THR B 195 SHEET 6 C 7 VAL B 144 PHE B 147 -1 N VAL B 145 O GLY B 167 SHEET 7 C 7 ILE B 223 LEU B 225 -1 O GLU B 224 N ARG B 146 LINK C LEU A 110 N CSD A 111 1555 1555 1.35 LINK C CSD A 111 N SER A 112 1555 1555 1.33 LINK C SER A 112 N CSO A 113 1555 1555 1.33 LINK C CSO A 113 N TYR A 114 1555 1555 1.33 LINK SG CYS A 108 CO CO A 301 1555 1555 2.32 LINK SG CSD A 111 CO CO A 301 1555 1555 2.10 LINK N SER A 112 CO CO A 301 1555 1555 2.00 LINK N CSO A 113 CO CO A 301 1555 1555 1.89 LINK SG CSO A 113 CO CO A 301 1555 1555 2.19 LINK CO CO A 301 O HOH A 527 1555 1555 2.30 SITE 1 AC1 5 CYS A 108 CSD A 111 SER A 112 CSO A 113 SITE 2 AC1 5 HOH A 527 CRYST1 65.683 65.683 184.796 90.00 90.00 120.00 P 32 2 1 6 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 0.015225 0.008790 0.000000 0.00000 SCALE2 0.000000 0.017580 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005411 0.00000