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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
