HEADER OXIDOREDUCTASE 15-JAN-07 2E81 TITLE CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES WITH BOUND TITLE 2 INTERMEDIATE HYDROXYLAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C-552; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AMMONIA-FORMING CYTOCHROME C NITRITE REDUCTASE, CYTOCHROME C COMPND 5 NITRITE REDUCTASE; COMPND 6 EC: 1.7.2.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: WOLINELLA SUCCINOGENES; SOURCE 3 ORGANISM_TAXID: 273121; SOURCE 4 STRAIN: DSM 1740 KEYWDS MULTIHEME CYTOCHROME, NITRITE REDUCTASE, REACTION INTERMEDIATE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR O.EINSLE,P.M.H.KRONECK REVDAT 6 06-NOV-24 2E81 1 REMARK REVDAT 5 25-OCT-23 2E81 1 REMARK LINK REVDAT 4 11-OCT-17 2E81 1 REMARK REVDAT 3 13-JUL-11 2E81 1 VERSN REVDAT 2 24-FEB-09 2E81 1 VERSN REVDAT 1 30-JAN-07 2E81 0 JRNL AUTH O.EINSLE,A.MESSERSCHMIDT,R.HUBER,P.M.H.KRONECK,F.NEESE JRNL TITL MECHANISM OF THE SIX-ELECTRON REDUCTION OF NITRITE TO JRNL TITL 2 AMMONIA BY CYTOCHROME C NITRITE REDUCTASE JRNL REF J.AM.CHEM.SOC. V. 124 11737 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 12296741 JRNL DOI 10.1021/JA0206487 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.EINSLE,A.MESSERSCHMIDT,P.STACH,G.P.BOURENKOV,H.D.BARTUNIK, REMARK 1 AUTH 2 R.HUBER,P.M.H.KRONECK REMARK 1 TITL STRUCTURE OF CYTOCHROME C NITRITE REDUCTASE REMARK 1 REF NATURE V. 400 476 1999 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 10440380 REMARK 1 DOI 10.1038/22802 REMARK 1 REFERENCE 2 REMARK 1 AUTH O.EINSLE,P.STACH,A.MESSERSCHMIDT,J.SIMON,A.KROEGER,R.HUBER, REMARK 1 AUTH 2 P.M.H.KRONECK REMARK 1 TITL CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES. REMARK 1 TITL 2 STRUCTURE AT 1.6 A RESOLUTION, INHIBITOR BINDING, AND REMARK 1 TITL 3 HEME-PACKING MOTIFS REMARK 1 REF J.BIOL.CHEM. V. 275 39608 2000 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 10984487 REMARK 1 DOI 10.1074/JBC.M006188200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 43459 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 SET) : 0.187 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2292 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3772 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 221 REMARK 3 SOLVENT ATOMS : 431 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.21000 REMARK 3 B22 (A**2) : -3.21000 REMARK 3 B33 (A**2) : 6.42100 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 2.259 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000026341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.05 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45781 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: 1FS7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 4000, 0.2M AMMONIUM SULFATE, REMARK 280 0.015M YTTRIUM CHLORIDE, 0.1M SODIUM ACETATE, PH 5.7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 59.94550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 59.94550 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.11200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 59.94550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.55600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 59.94550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 139.66800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 59.94550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 139.66800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.94550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.55600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 59.94550 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 59.94550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 93.11200 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 59.94550 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 59.94550 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 93.11200 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 59.94550 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 139.66800 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 59.94550 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 46.55600 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 59.94550 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 46.55600 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 59.94550 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 139.66800 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 59.94550 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 59.94550 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 93.11200 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 300 REMARK: BIOLOGICAL UNIT IS A DIMER, CREATED BY THE CRYSTALLOGRAPHIC REMARK 300 TWOFOLD AXIS. 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 16900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -322.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 119.89100 REMARK 350 BIOMT3 2 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 Y YT3 A 803 LIES ON A SPECIAL POSITION. 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 SER A 23 REMARK 465 ASN A 24 REMARK 465 ILE A 25 REMARK 465 ASN A 26 REMARK 465 GLU A 27 REMARK 465 ARG A 28 REMARK 465 GLU A 29 REMARK 465 LYS A 30 REMARK 465 GLU A 31 REMARK 465 ARG A 32 REMARK 465 VAL A 33 REMARK 465 ALA A 34 REMARK 465 LEU A 35 REMARK 465 ASN A 36 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 LYS A 226 CB CG CD CE NZ REMARK 480 LYS A 229 CD CE NZ REMARK 480 ARG A 331 CB CG CD NE CZ NH1 NH2 REMARK 480 LYS A 336 CG CD CE NZ REMARK 480 LYS A 342 CE NZ 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 OE2 GLU A 45 O HOH A 1932 12555 1.37 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 HIS A 40 40.69 -146.35 REMARK 500 THR A 132 -52.17 -28.27 REMARK 500 ILE A 166 110.85 -19.51 REMARK 500 HIS A 277 71.01 21.21 REMARK 500 ALA A 307 -32.95 77.88 REMARK 500 ASN A 321 49.23 -142.54 REMARK 500 MET A 327 24.05 -61.22 REMARK 500 SER A 333 133.91 -38.20 REMARK 500 PHE A 445 55.61 -144.54 REMARK 500 THR A 472 -84.49 -116.66 REMARK 500 THR A 505 -102.77 82.44 REMARK 500 LYS A 506 -159.95 -48.85 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 HEM A1510 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 102 NE2 REMARK 620 2 HEM A1510 NA 88.4 REMARK 620 3 HEM A1510 NB 96.4 90.7 REMARK 620 4 HEM A1510 NC 89.4 177.5 88.4 REMARK 620 5 HEM A1510 ND 88.1 89.2 175.5 91.8 REMARK 620 6 HIS A 215 NE2 177.5 92.6 81.4 89.5 94.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1508 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 134 NZ REMARK 620 2 HEM A1508 NA 90.4 REMARK 620 3 HEM A1508 NB 91.9 91.3 REMARK 620 4 HEM A1508 NC 85.4 175.6 90.1 REMARK 620 5 HEM A1508 ND 86.4 88.6 178.3 89.9 REMARK 620 6 HOA A 704 N 175.3 92.8 91.5 91.3 90.2 REMARK 620 7 HOA A 704 O 159.9 73.3 77.1 111.0 104.5 24.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1509 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 HEM A1509 NA 89.1 REMARK 620 3 HEM A1509 NB 88.3 90.3 REMARK 620 4 HEM A1509 NC 87.2 176.3 89.6 REMARK 620 5 HEM A1509 ND 92.3 90.3 179.1 89.7 REMARK 620 6 HIS A 313 NE2 174.9 90.9 86.6 92.8 92.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 513 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 GLU A 217 OE1 50.4 REMARK 620 3 TYR A 218 O 79.8 86.3 REMARK 620 4 LYS A 274 O 107.6 90.4 167.1 REMARK 620 5 GLN A 276 OE1 131.9 82.9 87.5 79.7 REMARK 620 6 HOH A1610 O 85.5 132.3 104.8 86.6 142.5 REMARK 620 7 HOH A1740 O 145.2 151.0 77.3 100.3 72.8 75.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1512 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 288 NE2 REMARK 620 2 HEM A1512 NA 88.3 REMARK 620 3 HEM A1512 NB 96.0 88.4 REMARK 620 4 HEM A1512 NC 93.1 178.5 91.8 REMARK 620 5 HEM A1512 ND 85.1 91.2 178.9 88.6 REMARK 620 6 HIS A 330 NE2 177.4 89.2 84.8 89.4 94.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1511 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 299 NE2 REMARK 620 2 HEM A1511 NA 89.0 REMARK 620 3 HEM A1511 NB 89.9 90.6 REMARK 620 4 HEM A1511 NC 90.4 179.3 89.4 REMARK 620 5 HEM A1511 ND 90.9 89.0 179.1 90.9 REMARK 620 6 HIS A 405 NE2 176.6 94.3 90.9 86.3 88.3 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 CA A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1512 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HOA A 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FS7 RELATED DB: PDB REMARK 900 CYTOCHROME C NITRITE REDUCTASE REMARK 900 RELATED ID: 1FS8 RELATED DB: PDB REMARK 900 CYTOCHROME C NITRITE REDUCTASE SULFATE COMPLEX REMARK 900 RELATED ID: 1FS9 RELATED DB: PDB REMARK 900 CYTOCHROME C NITRITE REDUCTASE AZIDE COMPLEX REMARK 900 RELATED ID: 2E80 RELATED DB: PDB REMARK 900 CYTOCHROME C NITRITE REDUCTASE WITH BOUND SUBSTRATE NITRITE DBREF 2E81 A 23 507 UNP Q9S1E5 NRFA_WOLSU 23 507 SEQRES 1 A 485 SER ASN ILE ASN GLU ARG GLU LYS GLU ARG VAL ALA LEU SEQRES 2 A 485 ASN LYS THR ALA HIS SER GLN GLY ILE GLU GLY LYS ALA SEQRES 3 A 485 MET SER GLU GLU TRP ALA ARG TYR TYR PRO ARG GLN PHE SEQRES 4 A 485 ASP SER TRP LYS LYS THR LYS GLU SER ASP ASN ILE THR SEQRES 5 A 485 ASP MET LEU LYS GLU LYS PRO ALA LEU VAL VAL ALA TRP SEQRES 6 A 485 ALA GLY TYR PRO PHE SER LYS ASP TYR ASN ALA PRO ARG SEQRES 7 A 485 GLY HIS TYR TYR ALA LEU GLN ASP ASN ILE ASN THR LEU SEQRES 8 A 485 ARG THR GLY ALA PRO VAL ASP GLY LYS THR GLY PRO LEU SEQRES 9 A 485 PRO SER ALA CYS TRP THR CYS LYS SER PRO ASP VAL PRO SEQRES 10 A 485 ARG ILE ILE GLU GLN ASP GLY GLU LEU GLU TYR PHE THR SEQRES 11 A 485 GLY LYS TRP ALA LYS TYR GLY ASP GLU ILE VAL ASN THR SEQRES 12 A 485 ILE GLY CYS TYR ASN CYS HIS ASP ASP LYS SER ALA GLU SEQRES 13 A 485 LEU LYS SER LYS VAL PRO TYR LEU ASP ARG GLY LEU SER SEQRES 14 A 485 ALA ALA GLY PHE LYS THR PHE ALA GLU SER THR HIS GLN SEQRES 15 A 485 GLU LYS ARG SER LEU VAL CYS ALA GLN CYS HIS VAL GLU SEQRES 16 A 485 TYR TYR PHE LYS LYS THR GLU TRP LYS ASP ASP LYS GLY SEQRES 17 A 485 VAL ASP LYS THR ALA MET VAL VAL THR LEU PRO TRP SER SEQRES 18 A 485 LYS GLY ILE SER THR GLU GLN MET GLU ALA TYR TYR ASP SEQRES 19 A 485 GLU ILE ASN PHE ALA ASP TRP THR HIS GLY ILE SER LYS SEQRES 20 A 485 THR PRO MET LEU LYS ALA GLN HIS PRO ASP TRP GLU LEU SEQRES 21 A 485 TYR LYS THR GLY ILE HIS GLY GLN LYS GLY VAL SER CYS SEQRES 22 A 485 ALA ASP CYS HIS MET PRO TYR THR GLN GLU GLY ALA VAL SEQRES 23 A 485 LYS TYR SER ASP HIS LYS VAL GLY ASN PRO LEU ASP ASN SEQRES 24 A 485 MET ASP LYS SER CYS MET ASN CYS HIS ARG GLU SER GLU SEQRES 25 A 485 GLN LYS LEU LYS ASP ILE VAL LYS GLN LYS PHE GLU ARG SEQRES 26 A 485 LYS GLU PHE LEU GLN ASP ILE ALA PHE ASP ASN ILE GLY SEQRES 27 A 485 LYS ALA HIS LEU GLU THR GLY LYS ALA MET GLU LEU GLY SEQRES 28 A 485 ALA THR ASP ALA GLU LEU LYS GLU ILE ARG THR HIS ILE SEQRES 29 A 485 ARG HIS ALA GLN TRP ARG ALA ASP MET ALA ILE ALA GLY SEQRES 30 A 485 HIS GLY SER PHE PHE HIS ALA PRO GLU GLU VAL LEU ARG SEQRES 31 A 485 LEU LEU ALA SER GLY ASN GLU GLU ALA GLN LYS ALA ARG SEQRES 32 A 485 ILE LYS LEU VAL LYS VAL LEU ALA LYS TYR GLY ALA ILE SEQRES 33 A 485 ASP TYR VAL ALA PRO ASP PHE GLU THR LYS GLU LYS ALA SEQRES 34 A 485 GLN LYS LEU ALA LYS VAL ASP MET GLU ALA PHE ILE ALA SEQRES 35 A 485 GLU LYS LEU LYS PHE LYS GLN THR LEU GLU GLN GLU TRP SEQRES 36 A 485 LYS LYS GLN ALA ILE ALA LYS GLY ARG LEU ASN PRO GLU SEQRES 37 A 485 SER LEU LYS GLY VAL ASP GLU LYS SER SER TYR TYR ASP SEQRES 38 A 485 LYS THR LYS LYS HET CA A 513 1 HET YT3 A 801 1 HET YT3 A 802 1 HET YT3 A 803 1 HET HEM A1508 43 HET HEM A1509 43 HET HEM A1510 43 HET HEM A1511 43 HET HEM A1512 43 HET HOA A 704 2 HETNAM CA CALCIUM ION HETNAM YT3 YTTRIUM (III) ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM HOA HYDROXYAMINE HETSYN HEM HEME FORMUL 2 CA CA 2+ FORMUL 3 YT3 3(Y 3+) FORMUL 6 HEM 5(C34 H32 FE N4 O4) FORMUL 11 HOA H3 N O FORMUL 12 HOH *431(H2 O) HELIX 1 1 MET A 49 ALA A 54 5 6 HELIX 2 2 TYR A 57 LYS A 66 1 10 HELIX 3 3 THR A 67 SER A 70 5 4 HELIX 4 4 ASP A 75 LYS A 80 1 6 HELIX 5 5 PRO A 81 TRP A 87 1 7 HELIX 6 6 TYR A 90 LYS A 94 5 5 HELIX 7 7 GLY A 101 TYR A 103 5 3 HELIX 8 8 TYR A 104 THR A 112 1 9 HELIX 9 9 LEU A 113 GLY A 116 5 4 HELIX 10 10 PRO A 127 THR A 132 5 6 HELIX 11 11 PRO A 136 GLY A 146 1 11 HELIX 12 12 GLY A 146 PHE A 151 1 6 HELIX 13 13 LYS A 154 GLY A 159 5 6 HELIX 14 14 GLY A 167 HIS A 172 1 6 HELIX 15 15 PRO A 184 ALA A 193 1 10 HELIX 16 16 THR A 202 GLN A 213 1 12 HELIX 17 17 SER A 247 ILE A 258 1 12 HELIX 18 18 PRO A 278 GLY A 286 1 9 HELIX 19 19 GLY A 286 LYS A 291 1 6 HELIX 20 20 SER A 294 MET A 300 1 7 HELIX 21 21 ASN A 317 ASP A 320 5 4 HELIX 22 22 ASN A 321 CYS A 326 1 6 HELIX 23 23 SER A 333 GLY A 373 1 41 HELIX 24 24 THR A 375 ALA A 398 1 24 HELIX 25 25 GLY A 401 ALA A 406 1 6 HELIX 26 26 ALA A 406 TYR A 435 1 30 HELIX 27 27 THR A 447 ALA A 455 1 9 HELIX 28 28 ASP A 458 THR A 472 1 15 HELIX 29 29 THR A 472 LYS A 484 1 13 HELIX 30 30 ASN A 488 LYS A 493 5 6 SHEET 1 A 2 TYR A 219 LYS A 226 0 SHEET 2 A 2 ASP A 232 THR A 239 -1 O ALA A 235 N THR A 223 SHEET 1 B 2 TRP A 263 THR A 264 0 SHEET 2 B 2 PRO A 271 MET A 272 -1 O MET A 272 N TRP A 263 SHEET 1 C 2 TYR A 302 GLU A 305 0 SHEET 2 C 2 VAL A 308 SER A 311 -1 O VAL A 308 N GLU A 305 LINK SG CYS A 130 CAB HEM A1508 1555 1555 1.84 LINK SG CYS A 133 CAC HEM A1508 1555 1555 1.83 LINK SG CYS A 168 CAB HEM A1509 1555 1555 1.81 LINK SG CYS A 171 CAC HEM A1509 1555 1555 1.80 LINK SG CYS A 211 CAB HEM A1510 1555 1555 1.83 LINK SG CYS A 214 CAC HEM A1510 1555 1555 1.82 LINK SG CYS A 295 CAB HEM A1511 1555 1555 1.82 LINK SG CYS A 298 CAC HEM A1511 1555 1555 1.84 LINK SG CYS A 326 CAB HEM A1512 1555 1555 1.77 LINK SG CYS A 329 CAC HEM A1512 1555 1555 1.81 LINK NE2 HIS A 102 FE HEM A1510 1555 1555 2.01 LINK NZ LYS A 134 FE HEM A1508 1555 1555 2.13 LINK NE2 HIS A 172 FE HEM A1509 1555 1555 1.96 LINK NE2 HIS A 215 FE HEM A1510 1555 1555 2.03 LINK OE2 GLU A 217 CA CA A 513 1555 1555 2.47 LINK OE1 GLU A 217 CA CA A 513 1555 1555 2.66 LINK O TYR A 218 CA CA A 513 1555 1555 2.51 LINK O LYS A 274 CA CA A 513 1555 1555 2.35 LINK OE1 GLN A 276 CA CA A 513 1555 1555 2.39 LINK NE2 HIS A 288 FE HEM A1512 1555 1555 2.03 LINK NE2 HIS A 299 FE HEM A1511 1555 1555 2.03 LINK NE2 HIS A 313 FE HEM A1509 1555 1555 1.99 LINK NE2 HIS A 330 FE HEM A1512 1555 1555 2.00 LINK NE2 HIS A 405 FE HEM A1511 1555 1555 2.06 LINK CA CA A 513 O HOH A1610 1555 1555 2.40 LINK CA CA A 513 O HOH A1740 1555 1555 2.45 LINK N HOA A 704 FE HEM A1508 1555 1555 1.71 LINK O HOA A 704 FE HEM A1508 1555 1555 2.76 SITE 1 AC1 6 GLU A 217 TYR A 218 LYS A 274 GLN A 276 SITE 2 AC1 6 HOH A1610 HOH A1740 SITE 1 AC2 7 GLU A 52 ASP A 444 HOH A1683 HOH A1833 SITE 2 AC2 7 HOH A1834 HOH A1835 HOH A1839 SITE 1 AC3 7 PRO A 99 HEM A1510 HEM A1511 HOH A1693 SITE 2 AC3 7 HOH A1752 HOH A1842 HOH A1843 SITE 1 AC4 3 GLU A 408 HEM A1512 HOH A1899 SITE 1 AC5 25 TYR A 96 ASN A 97 ASP A 108 ASN A 109 SITE 2 AC5 25 THR A 112 ARG A 114 THR A 115 LEU A 126 SITE 3 AC5 25 CYS A 130 CYS A 133 LYS A 134 CYS A 214 SITE 4 AC5 25 HIS A 215 TYR A 218 HIS A 277 ALA A 398 SITE 5 AC5 25 HIS A 400 HOA A 704 HEM A1510 HOH A1552 SITE 6 AC5 25 HOH A1555 HOH A1576 HOH A1578 HOH A1582 SITE 7 AC5 25 HOH A1628 SITE 1 AC6 17 TYR A 57 GLN A 60 TRP A 64 GLY A 167 SITE 2 AC6 17 CYS A 168 CYS A 171 HIS A 172 LEU A 179 SITE 3 AC6 17 HIS A 203 ARG A 207 MET A 300 TYR A 302 SITE 4 AC6 17 TYR A 310 SER A 311 HIS A 313 HEM A1510 SITE 5 AC6 17 HOH A1877 SITE 1 AC7 24 SER A 70 PRO A 99 ARG A 100 GLY A 101 SITE 2 AC7 24 HIS A 102 TYR A 104 ALA A 105 ASP A 108 SITE 3 AC7 24 CYS A 133 LYS A 134 ILE A 166 VAL A 210 SITE 4 AC7 24 CYS A 211 CYS A 214 HIS A 215 VAL A 315 SITE 5 AC7 24 GLY A 316 YT3 A 802 HEM A1508 HEM A1509 SITE 6 AC7 24 HEM A1511 HOH A1550 HOH A1551 HOH A1752 SITE 1 AC8 20 PRO A 99 TRP A 280 TYR A 283 HIS A 288 SITE 2 AC8 20 SER A 294 CYS A 295 CYS A 298 HIS A 299 SITE 3 AC8 20 ASN A 317 LEU A 319 HIS A 400 GLY A 401 SITE 4 AC8 20 PHE A 403 PHE A 404 HIS A 405 YT3 A 802 SITE 5 AC8 20 HEM A1510 HEM A1512 HOH A1753 HOH A1843 SITE 1 AC9 15 ILE A 287 HIS A 288 VAL A 293 PRO A 318 SITE 2 AC9 15 SER A 325 CYS A 326 CYS A 329 HIS A 330 SITE 3 AC9 15 LEU A 337 LYS A 344 PRO A 407 YT3 A 803 SITE 4 AC9 15 HEM A1511 HOH A1754 HOH A1899 SITE 1 BC1 6 ARG A 114 HIS A 277 HEM A1508 HOH A1513 SITE 2 BC1 6 HOH A1514 HOH A1515 CRYST1 119.891 119.891 186.224 90.00 90.00 90.00 I 41 2 2 16 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 0.008341 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008341 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005370 0.00000