HEADER OXIDOREDUCTASE 11-MAR-14 4CSZ TITLE STRUCTURE OF F306C MUTANT OF NITRITE REDUCTASE FROM ACHROMOBACTER TITLE 2 XYLOSOXIDANS WITH NITRITE BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.7.2.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER XYLOSOXIDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 STRAIN: IW2 IWASAKI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26 KEYWDS OXIDOREDUCTASE, ELECTRON TRANSFER, MICROBIAL ATP-GENERATING KEYWDS 2 RESPIRATORY DENTRIFICATION PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR N.G.H.LEFERINK,S.V.ANTONYUK,J.A.HOUWMAN,N.S.SCRUTTON,R.READY, AUTHOR 2 S.S.HASNAIN REVDAT 2 20-DEC-23 4CSZ 1 REMARK LINK REVDAT 1 30-JUL-14 4CSZ 0 JRNL AUTH N.G.H.LEFERINK,S.V.ANTONYUK,J.A.HOUWMAN,N.S.SCRUTTON, JRNL AUTH 2 R.R.EADY,S.S.HASNAIN JRNL TITL IMPACT OF RESIDUES REMOTE FROM THE CATALYTIC CENTRE ON JRNL TITL 2 ENZYME CATALYSIS OF COPPER NITRITE REDUCTASE. JRNL REF NAT.COMMUN. V. 5 4395 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 25022223 JRNL DOI 10.1038/NCOMMS5395 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 41268 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2185 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3021 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 182 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2562 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 308 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : -1.43000 REMARK 3 B12 (A**2) : 0.22000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.573 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2712 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2605 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3697 ; 1.542 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6029 ; 0.786 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 352 ; 7.147 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 113 ;34.749 ;24.071 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 446 ;12.619 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;13.352 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 403 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3078 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 601 ; 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): 1357 ; 1.875 ; 2.750 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1356 ; 1.874 ; 2.746 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1699 ; 2.750 ; 4.114 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1355 ; 1.992 ; 2.937 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4CSZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1290059958. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43456 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 52.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: PDB ENTRY 2CSP REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG550 MME, 50 MM ZNSO4, AND 50 MM REMARK 280 MES BUFFER, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.78500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.85663 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.00367 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 44.78500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 25.85663 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.00367 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 44.78500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 25.85663 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.00367 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.71326 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 96.00733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 51.71326 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 96.00733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 51.71326 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 96.00733 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -715.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2076 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2125 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2262 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2272 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2313 LIES ON A SPECIAL POSITION. 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 ZN ZN A 1342 O HOH A 2091 1.46 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 A 2251 O HOH A 2251 3555 2.01 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 ASP A 92 CB - CG - OD1 ANGL. DEV. = 5.5 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 GLN A 24 -106.01 -86.05 REMARK 500 ASN A 90 -166.28 -164.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 300 ASN A 301 146.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2076 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A2132 DISTANCE = 5.98 ANGSTROMS 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 ZN A1345 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 8 NE2 REMARK 620 2 HOH A2004 O 81.6 REMARK 620 3 HOH A2009 O 71.0 147.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1342 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 70 ND1 REMARK 620 2 ASP A 73 OD2 114.1 REMARK 620 3 HOH A2041 O 105.6 138.7 REMARK 620 4 HOH A2043 O 129.1 100.5 42.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A1337 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 130 SG 127.0 REMARK 620 3 HIS A 139 ND1 100.7 119.8 REMARK 620 4 MET A 144 SD 82.0 111.2 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A1338 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 129 NE2 104.2 REMARK 620 3 HIS A 300 NE2 104.7 107.6 REMARK 620 4 NO2 A1340 O2 148.4 103.5 80.9 REMARK 620 5 NO2 A1340 N 129.1 97.1 112.0 31.3 REMARK 620 6 NO2 A1340 O1 87.7 120.8 125.3 65.0 42.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 165 NE2 REMARK 620 2 ASP A 167 OD2 84.8 REMARK 620 3 ZN A1339 ZN 44.4 50.5 REMARK 620 4 ZN A1339 ZN 83.0 35.5 71.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1339 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 165 NE2 REMARK 620 2 ASP A 167 OD1 98.2 REMARK 620 3 ASP A 167 OD2 129.5 59.4 REMARK 620 4 HOH A2214 O 72.9 48.4 107.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1344 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 306 SG REMARK 620 2 HOH A2287 O 103.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1341 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 307 OE2 REMARK 620 2 HOH A2148 O 161.0 REMARK 620 3 HOH A2289 O 86.1 106.0 REMARK 620 4 HOH A2290 O 90.4 71.3 114.5 REMARK 620 5 HOH A2291 O 90.1 106.2 80.0 165.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1343 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 313 NE2 REMARK 620 2 HOH A2293 O 99.5 REMARK 620 3 HOH A2315 O 152.8 70.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 1338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO2 A 1340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1344 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1345 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 1346 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CSP RELATED DB: PDB REMARK 900 STRUCTURE OF THE F306C MUTANT OF NITRITE REDUCTASE FROM REMARK 900 ACHROMOBACTER XYLOSOXIDANS REMARK 999 REMARK 999 SEQUENCE REMARK 999 MUTATION F306C DBREF 4CSZ A 2 336 UNP O68601 O68601_ALCXX 26 360 SEQADV 4CSZ CYS A 306 UNP O68601 PHE 330 ENGINEERED MUTATION SEQRES 1 A 335 ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU VAL SEQRES 2 A 335 ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR LYS SEQRES 3 A 335 SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE GLU SEQRES 4 A 335 GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR LEU SEQRES 5 A 335 GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO THR SEQRES 6 A 335 LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR LEU SEQRES 7 A 335 VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL ASP SEQRES 8 A 335 PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS LEU SEQRES 9 A 335 THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG PHE SEQRES 10 A 335 LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS CYS ALA SEQRES 11 A 335 PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY MET SEQRES 12 A 335 SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU LYS SEQRES 13 A 335 ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA TYR SEQRES 14 A 335 THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY PRO SEQRES 15 A 335 ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SER SEQRES 16 A 335 TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR PRO SEQRES 17 A 335 SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU THR SEQRES 18 A 335 GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR VAL SEQRES 19 A 335 LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG PRO SEQRES 20 A 335 HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU THR SEQRES 21 A 335 GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU THR SEQRES 22 A 335 TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU TYR SEQRES 23 A 335 THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN HIS SEQRES 24 A 335 ASN LEU ILE GLU ALA CYS GLU LEU GLY ALA ALA GLY HIS SEQRES 25 A 335 ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET LYS SEQRES 26 A 335 GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG HET ZN A 504 1 HET CU A1337 1 HET CU A1338 1 HET ZN A1339 1 HET NO2 A1340 3 HET ZN A1341 1 HET ZN A1342 1 HET ZN A1343 1 HET ZN A1344 1 HET ZN A1345 1 HET PEG A1346 7 HETNAM ZN ZINC ION HETNAM CU COPPER (II) ION HETNAM NO2 NITRITE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 ZN 7(ZN 2+) FORMUL 3 CU 2(CU 2+) FORMUL 6 NO2 N O2 1- FORMUL 12 PEG C4 H10 O3 FORMUL 13 HOH *308(H2 O) HELIX 1 1 ASP A 2 LEU A 6 5 5 HELIX 2 2 GLY A 98 THR A 106 5 9 HELIX 3 3 MET A 135 SER A 142 1 8 HELIX 4 4 THR A 192 THR A 206 1 15 HELIX 5 5 THR A 222 ALA A 226 5 5 HELIX 6 6 ASN A 301 GLU A 307 1 7 SHEET 1 AA 2 HIS A 8 LYS A 10 0 SHEET 2 AA 2 VAL A 32 VAL A 45 1 O VAL A 32 N THR A 9 SHEET 1 AB 2 THR A 52 PHE A 58 0 SHEET 2 AB 2 VAL A 32 VAL A 45 -1 O GLU A 40 N THR A 57 SHEET 1 AC 4 GLU A 112 LYS A 119 0 SHEET 2 AC 4 TYR A 74 ASN A 81 -1 O VAL A 75 N PHE A 118 SHEET 3 AC 4 VAL A 32 VAL A 45 1 O VAL A 33 N GLN A 76 SHEET 4 AC 4 THR A 52 PHE A 58 -1 O LEU A 53 N MET A 44 SHEET 1 AD 4 GLU A 112 LYS A 119 0 SHEET 2 AD 4 TYR A 74 ASN A 81 -1 O VAL A 75 N PHE A 118 SHEET 3 AD 4 VAL A 32 VAL A 45 1 O VAL A 33 N GLN A 76 SHEET 4 AD 4 HIS A 8 LYS A 10 1 O THR A 9 N GLU A 34 SHEET 1 AE 4 LEU A 67 HIS A 70 0 SHEET 2 AE 4 SER A 145 LEU A 151 1 O THR A 147 N LEU A 67 SHEET 3 AE 4 GLY A 124 HIS A 129 -1 O GLY A 124 N VAL A 150 SHEET 4 AE 4 ASP A 92 PHE A 93 -1 O ASP A 92 N HIS A 129 SHEET 1 AF 6 HIS A 211 PHE A 214 0 SHEET 2 AF 6 ARG A 168 LEU A 177 -1 O PHE A 175 N VAL A 213 SHEET 3 AF 6 THR A 234 GLN A 241 1 O LEU A 236 N TYR A 170 SHEET 4 AF 6 SER A 281 THR A 288 -1 O SER A 281 N GLN A 241 SHEET 5 AF 6 GLY A 255 TRP A 259 -1 N ASP A 256 O LEU A 286 SHEET 6 AF 6 GLN A 269 LEU A 272 -1 O GLN A 269 N VAL A 258 SHEET 1 AG 4 LEU A 227 LYS A 230 0 SHEET 2 AG 4 ALA A 311 GLU A 317 1 O HIS A 313 N LEU A 227 SHEET 3 AG 4 GLY A 293 ASN A 299 -1 O GLY A 293 N VAL A 316 SHEET 4 AG 4 PRO A 248 LEU A 250 -1 O HIS A 249 N LEU A 298 LINK NE2 HIS A 8 ZN ZN A1345 1555 1555 2.27 LINK ND1 HIS A 70 ZN ZN A1342 1555 1555 2.41 LINK OD2 ASP A 73 ZN ZN A1342 1555 1555 2.24 LINK ND1 HIS A 89 CU CU A1337 1555 1555 2.19 LINK NE2 HIS A 94 CU CU A1338 1555 1555 2.08 LINK NE2 HIS A 129 CU CU A1338 1555 1555 2.03 LINK SG CYS A 130 CU CU A1337 1555 1555 2.06 LINK ND1 HIS A 139 CU CU A1337 1555 1555 2.01 LINK SD MET A 144 CU CU A1337 1555 1555 2.68 LINK NE2 HIS A 165 ZN ZN A 504 9554 1555 2.61 LINK NE2 HIS A 165 ZN ZN A1339 1555 1555 1.88 LINK OD2 ASP A 167 ZN ZN A 504 9554 1555 2.49 LINK OD1 ASP A 167 ZN ZN A1339 1555 1555 2.37 LINK OD2 ASP A 167 ZN ZN A1339 1555 1555 1.92 LINK NE2 HIS A 300 CU CU A1338 3555 1555 2.15 LINK SG CYS A 306 ZN ZN A1344 1555 1555 2.03 LINK OE2 GLU A 307 ZN ZN A1341 3555 1555 2.01 LINK NE2 HIS A 313 ZN ZN A1343 1555 1555 2.19 LINK ZN ZN A 504 ZN ZN A1339 1555 9554 1.43 LINK ZN ZN A 504 ZN ZN A1339 5555 1555 1.43 LINK CU CU A1338 O2 NO2 A1340 1555 1555 2.38 LINK CU CU A1338 N NO2 A1340 1555 1555 1.99 LINK CU CU A1338 O1 NO2 A1340 1555 1555 1.94 LINK ZN ZN A1339 O HOH A2214 1555 9554 1.72 LINK ZN ZN A1341 O HOH A2148 1555 1555 2.15 LINK ZN ZN A1341 O HOH A2289 1555 3555 2.15 LINK ZN ZN A1341 O HOH A2290 1555 3555 2.46 LINK ZN ZN A1341 O HOH A2291 1555 3555 2.21 LINK ZN ZN A1342 O HOH A2041 1555 1555 2.29 LINK ZN ZN A1342 O HOH A2043 1555 1555 2.33 LINK ZN ZN A1343 O HOH A2293 1555 1555 2.02 LINK ZN ZN A1343 O HOH A2315 1555 1555 2.40 LINK ZN ZN A1344 O HOH A2287 1555 1555 2.47 LINK ZN ZN A1345 O HOH A2004 1555 1555 1.71 LINK ZN ZN A1345 O HOH A2009 1555 1555 1.80 CISPEP 1 PRO A 16 PRO A 17 0 5.26 CISPEP 2 MET A 62 PRO A 63 0 -9.94 SITE 1 AC1 4 HIS A 89 CYS A 130 HIS A 139 MET A 144 SITE 1 AC2 5 ASP A 92 HIS A 94 HIS A 129 HIS A 300 SITE 2 AC2 5 NO2 A1340 SITE 1 AC3 5 HIS A 165 ASP A 167 GLU A 195 ZN A 504 SITE 2 AC3 5 HOH A2214 SITE 1 AC4 7 HIS A 165 ASP A 167 GLU A 195 THR A 234 SITE 2 AC4 7 ZN A1339 HOH A2214 HOH A2244 SITE 1 AC5 7 ASP A 92 HIS A 94 HIS A 129 HIS A 249 SITE 2 AC5 7 ILE A 251 HIS A 300 CU A1338 SITE 1 AC6 5 GLU A 307 HOH A2148 HOH A2289 HOH A2290 SITE 2 AC6 5 HOH A2291 SITE 1 AC7 5 HIS A 70 ASP A 73 HOH A2041 HOH A2043 SITE 2 AC7 5 HOH A2091 SITE 1 AC8 4 HIS A 313 HOH A2293 HOH A2294 HOH A2315 SITE 1 AC9 2 CYS A 306 HOH A2287 SITE 1 BC1 4 ASP A 4 HIS A 8 HOH A2004 HOH A2009 SITE 1 BC2 5 ASP A 121 ARG A 122 ASP A 256 LYS A 290 SITE 2 BC2 5 HOH A2256 CRYST1 89.570 89.570 144.011 90.00 90.00 120.00 H 3 9 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 0.011164 0.006446 0.000000 0.00000 SCALE2 0.000000 0.012892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006944 0.00000