PDB Short entry for 3X26 HEADER LYASE 10-DEC-14 3X26 TITLE CRYSTAL STRUCTURE OF NITRILE HYDRATASE MUTANT BR56K COMPLEXED WITH TITLE 2 TRIMETHYLACETONITRILE, PHOTO-ACTIVATED FOR 5 MIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRILE HYDRATASE SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NHASE, NITRILASE; COMPND 5 EC: 4.2.1.84; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NITRILE HYDRATASE SUBUNIT BETA; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: NHASE, NITRILASE; COMPND 11 EC: 4.2.1.84; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS ERYTHROPOLIS; SOURCE 3 ORGANISM_TAXID: 1833; SOURCE 4 GENE: NTHA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: RHODOCOCCUS ERYTHROPOLIS; SOURCE 9 ORGANISM_TAXID: 1833; SOURCE 10 GENE: NTHB, NHA2; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDRATASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.YAMANAKA,K.HASHIMOTO,K.NOGUCHI,M.YOHDA,M.ODAKA REVDAT 1 27-JAN-16 3X26 0 JRNL AUTH Y.YAMANAKA,Y.KATO,K.HASHIMOTO,K.IIDA,K.NAGASAWA,H.NAKAYAMA, JRNL AUTH 2 N.DOHMAE,K.NOGUCHI,T.NOGUCHI,M.YOHDA,M.ODAKA JRNL TITL TIME-RESOLVED CRYSTALLOGRAPHY OF THE REACTION INTERMEDIATE JRNL TITL 2 OF NITRILE HYDRATASE: REVEALING A ROLE FOR THE JRNL TITL 3 CYSTEINESULFENIC ACID LIGAND AS A CATALYTIC NUCLEOPHILE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 10763 2015 JRNL REFN ISSN 1433-7851 JRNL PMID 26333053 JRNL DOI 10.1002/ANIE.201502731 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 88068 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4632 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) : 1.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4427 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 250 REMARK 3 BIN FREE R VALUE : 0.2120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3201 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 312 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.768 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3352 ; 0.028 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3095 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4579 ; 2.525 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7141 ; 1.005 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 421 ; 6.106 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;34.298 ;23.203 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 514 ;10.771 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;22.776 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 493 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3832 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 761 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 REMARK 4 REMARK 4 3X26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-14. REMARK 100 THE RCSB ID CODE IS RCSB097084. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-12 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-1A 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 : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97343 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 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 (%) : 96.6 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) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.3M MGCL2, 0.1M TRIS- REMARK 280 HCL PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.93050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.97650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.93050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.97650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 8200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 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 0 REMARK 465 SER A 1 REMARK 465 VAL A 2 REMARK 465 THR A 3 REMARK 465 ILE A 4 REMARK 465 ASP A 5 REMARK 465 HIS A 6 REMARK 465 THR A 7 REMARK 465 THR A 8 REMARK 465 VAL A 206 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 GLU A 9 CD GLU A 9 OE1 -0.130 REMARK 500 GLU A 150 CD GLU A 150 OE1 -0.072 REMARK 500 GLU B 110 CD GLU B 110 OE2 -0.085 REMARK 500 ARG B 141 CZ ARG B 141 NH2 -0.087 REMARK 500 ASP B 195 CG ASP B 195 OD2 -0.142 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 21 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 30 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 LYS A 32 CD - CE - NZ ANGL. DEV. = 14.9 DEGREES REMARK 500 PHE A 51 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 70 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 99 OD1 - CG - OD2 ANGL. DEV. = 12.4 DEGREES REMARK 500 ASP A 99 CB - CG - OD2 ANGL. DEV. = -9.0 DEGREES REMARK 500 ARG A 135 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 135 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 158 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP B 6 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 TYR B 37 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 TYR B 37 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 LEU B 47 CB - CG - CD1 ANGL. DEV. = 10.7 DEGREES REMARK 500 GLU B 54 OE1 - CD - OE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG B 61 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 107 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 114 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 130 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 130 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 GLU B 205 OE1 - CD - OE2 ANGL. DEV. = 8.6 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 112 -93.89 -174.97 REMARK 500 SER A 113 3.71 -162.98 REMARK 500 ALA A 164 -133.53 -131.10 REMARK 500 PRO A 204 -178.02 -64.27 REMARK 500 ARG B 141 48.22 -98.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 141 0.08 SIDE CHAIN 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 FE A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CSO A 114 N REMARK 620 2 SER A 113 N 81.2 REMARK 620 3 CSD A 112 SG 177.1 97.1 REMARK 620 4 CSO A 114 SG 88.7 168.7 93.2 REMARK 620 5 CYS A 109 SG 92.8 91.3 89.6 84.1 REMARK 620 6 HOH A 556 O 93.2 95.3 84.6 90.4 171.7 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 FE A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WVD RELATED DB: PDB REMARK 900 RELATED ID: 3WVE RELATED DB: PDB REMARK 900 RELATED ID: 3X20 RELATED DB: PDB REMARK 900 RELATED ID: 3X24 RELATED DB: PDB REMARK 900 RELATED ID: 3X25 RELATED DB: PDB REMARK 900 RELATED ID: 3X28 RELATED DB: PDB DBREF 3X26 A 0 206 UNP P13448 NHAA_RHOER 1 207 DBREF 3X26 B 1 212 UNP P13449 NHAB_RHOER 1 212 SEQADV 3X26 LYS B 56 UNP P13449 ARG 56 ENGINEERED MUTATION SEQRES 1 A 207 MET SER VAL THR ILE ASP HIS THR THR GLU ASN ALA ALA SEQRES 2 A 207 PRO ALA GLN ALA PRO VAL SER ASP ARG ALA TRP ALA LEU SEQRES 3 A 207 PHE ARG ALA LEU ASP GLY LYS GLY LEU VAL PRO ASP GLY SEQRES 4 A 207 TYR VAL GLU GLY TRP LYS LYS THR PHE GLU GLU ASP PHE SEQRES 5 A 207 SER PRO ARG ARG GLY ALA GLU LEU VAL ALA ARG ALA TRP SEQRES 6 A 207 THR ASP PRO GLU PHE ARG GLN LEU LEU LEU THR ASP GLY SEQRES 7 A 207 THR ALA ALA VAL ALA GLN TYR GLY TYR LEU GLY PRO GLN SEQRES 8 A 207 GLY GLU TYR ILE VAL ALA VAL GLU ASP THR PRO THR LEU SEQRES 9 A 207 LYS ASN VAL ILE VAL CYS SER LEU CSD SER CSO THR ALA SEQRES 10 A 207 TRP PRO ILE LEU GLY LEU PRO PRO THR TRP TYR LYS SER SEQRES 11 A 207 PHE GLU TYR ARG ALA ARG VAL VAL ARG GLU PRO ARG LYS SEQRES 12 A 207 VAL LEU SER GLU MET GLY THR GLU ILE ALA SER ASP ILE SEQRES 13 A 207 GLU ILE ARG VAL TYR ASP THR THR ALA GLU THR ARG TYR SEQRES 14 A 207 MET VAL LEU PRO GLN ARG PRO ALA GLY THR GLU GLY TRP SEQRES 15 A 207 SER GLN GLU GLN LEU GLN GLU ILE VAL THR LYS ASP CYS SEQRES 16 A 207 LEU ILE GLY VAL ALA ILE PRO GLN VAL PRO THR VAL SEQRES 1 B 212 MET ASP GLY VAL HIS ASP LEU ALA GLY VAL GLN GLY PHE SEQRES 2 B 212 GLY LYS VAL PRO HIS THR VAL ASN ALA ASP ILE GLY PRO SEQRES 3 B 212 THR PHE HIS ALA GLU TRP GLU HIS LEU PRO TYR SER LEU SEQRES 4 B 212 MET PHE ALA GLY VAL ALA GLU LEU GLY ALA PHE SER VAL SEQRES 5 B 212 ASP GLU VAL LYS TYR VAL VAL GLU ARG MET GLU PRO ARG SEQRES 6 B 212 HIS TYR MET MET THR PRO TYR TYR GLU ARG TYR VAL ILE SEQRES 7 B 212 GLY VAL ALA THR LEU MET VAL GLU LYS GLY ILE LEU THR SEQRES 8 B 212 GLN ASP GLU LEU GLU SER LEU ALA GLY GLY PRO PHE PRO SEQRES 9 B 212 LEU SER ARG PRO SER GLU SER GLU GLY ARG PRO ALA PRO SEQRES 10 B 212 VAL GLU THR THR THR PHE GLU VAL GLY GLN ARG VAL ARG SEQRES 11 B 212 VAL ARG ASP GLU TYR VAL PRO GLY HIS ILE ARG MET PRO SEQRES 12 B 212 ALA TYR CYS ARG GLY ARG VAL GLY THR ILE SER HIS ARG SEQRES 13 B 212 THR THR GLU LYS TRP PRO PHE PRO ASP ALA ILE GLY HIS SEQRES 14 B 212 GLY ARG ASN ASP ALA GLY GLU GLU PRO THR TYR HIS VAL SEQRES 15 B 212 LYS PHE ALA ALA GLU GLU LEU PHE GLY SER ASP THR ASP SEQRES 16 B 212 GLY GLY SER VAL VAL VAL ASP LEU PHE GLU GLY TYR LEU SEQRES 17 B 212 GLU PRO ALA ALA MODRES 3X26 CSD A 112 CYS 3-SULFINOALANINE MODRES 3X26 CSO A 114 CYS S-HYDROXYCYSTEINE HET CSD A 112 8 HET CSO A 114 7 HET FE A 301 1 HET MG A 302 1 HET CL A 303 1 HET CL A 304 1 HET TAN B 301 6 HET MG B 302 1 HET CL B 303 1 HET CL B 304 1 HETNAM CSD 3-SULFINOALANINE HETNAM CSO S-HYDROXYCYSTEINE HETNAM FE FE (III) ION HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM TAN 2,2-DIMETHYLPROPANENITRILE HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE HETSYN TAN TRIMETHYLACETONITRILE FORMUL 1 CSD C3 H7 N O4 S FORMUL 1 CSO C3 H7 N O3 S FORMUL 3 FE FE 3+ FORMUL 4 MG 2(MG 2+) FORMUL 5 CL 4(CL 1-) FORMUL 7 TAN C5 H9 N FORMUL 11 HOH *312(H2 O) HELIX 1 1 PRO A 17 GLY A 31 1 15 HELIX 2 2 GLY A 38 ASP A 50 1 13 HELIX 3 3 SER A 52 ASP A 66 1 15 HELIX 4 4 ASP A 66 ASP A 76 1 11 HELIX 5 5 ASP A 76 TYR A 84 1 9 HELIX 6 6 ALA A 116 GLY A 121 1 6 HELIX 7 7 PRO A 124 LYS A 128 5 5 HELIX 8 8 SER A 129 VAL A 136 1 8 HELIX 9 9 GLU A 139 GLY A 148 1 10 HELIX 10 10 SER A 182 VAL A 190 1 9 HELIX 11 11 THR A 191 GLY A 197 1 7 HELIX 12 12 HIS B 34 GLU B 46 1 13 HELIX 13 13 SER B 51 ARG B 61 1 11 HELIX 14 14 GLU B 63 THR B 70 1 8 HELIX 15 15 PRO B 71 LYS B 87 1 17 HELIX 16 16 THR B 91 GLY B 100 1 10 HELIX 17 17 PRO B 143 ARG B 147 5 5 HELIX 18 18 PHE B 163 GLY B 168 1 6 HELIX 19 19 ALA B 186 GLY B 191 1 6 SHEET 1 A 2 ILE A 94 GLU A 98 0 SHEET 2 A 2 ARG A 167 LEU A 171 1 O LEU A 171 N VAL A 97 SHEET 1 B 7 LEU A 103 VAL A 108 0 SHEET 2 B 7 GLU A 156 ASP A 161 1 O GLU A 156 N LYS A 104 SHEET 3 B 7 SER B 198 PHE B 204 1 O VAL B 200 N VAL A 159 SHEET 4 B 7 THR B 179 ALA B 185 -1 N TYR B 180 O LEU B 203 SHEET 5 B 7 VAL B 150 ARG B 156 -1 N SER B 154 O HIS B 181 SHEET 6 B 7 ARG B 128 VAL B 131 -1 N VAL B 129 O GLY B 151 SHEET 7 B 7 LEU B 208 PRO B 210 -1 O GLU B 209 N ARG B 130 LINK C LEU A 111 N CSD A 112 1555 1555 1.33 LINK C CSD A 112 N SER A 113 1555 1555 1.35 LINK C SER A 113 N CSO A 114 1555 1555 1.28 LINK C CSO A 114 N THR A 115 1555 1555 1.32 LINK N CSO A 114 FE FE A 301 1555 1555 2.02 LINK N SER A 113 FE FE A 301 1555 1555 2.05 LINK SG CSD A 112 FE FE A 301 1555 1555 2.22 LINK SG CSO A 114 FE FE A 301 1555 1555 2.22 LINK SG CYS A 109 FE FE A 301 1555 1555 2.32 LINK FE FE A 301 O HOH A 556 1555 1555 1.99 LINK MG MG B 302 O HOH B 408 1555 1555 2.43 SITE 1 AC1 5 CYS A 109 CSD A 112 SER A 113 CSO A 114 SITE 2 AC1 5 HOH A 556 SITE 1 AC2 2 HOH B 476 HOH B 543 SITE 1 AC3 4 SER A 19 TRP A 23 GLU B 31 TRP B 32 SITE 1 AC4 5 THR A 125 TRP A 126 HOH B 474 HOH B 480 SITE 2 AC4 5 HOH B 523 SITE 1 AC5 5 TYR B 37 MET B 40 VAL B 55 TYR B 72 SITE 2 AC5 5 TYR B 76 SITE 1 AC6 1 HOH B 408 SITE 1 AC7 3 GLU B 134 TYR B 135 SER B 192 SITE 1 AC8 3 THR B 121 ARG B 132 LEU B 208 CRYST1 113.861 59.953 81.594 90.00 125.08 90.00 C 1 2 1 4 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 0.008783 0.000000 0.006168 0.00000 SCALE2 0.000000 0.016680 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014976 0.00000