HEADER OXIDOREDUCTASE 12-APR-00 1ET8 TITLE CRYSTAL STRUCTURE OF NITRITE REDUCTASE HIS255ASN MUTANT FROM TITLE 2 ALCALIGENES FAECALIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 40 - 376; COMPND 5 SYNONYM: CU-NIR; COMPND 6 EC: 1.7.99.3; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES FAECALIS; SOURCE 3 ORGANISM_TAXID: 511; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS GREEK KEY BETA BARREL DOMAIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BOULANGER,M.KUKIMOTO,M.NISHIYAMA,S.HORINOUCHI,M.E.P.MURPHY REVDAT 6 07-FEB-24 1ET8 1 REMARK REVDAT 5 03-NOV-21 1ET8 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1ET8 1 VERSN REVDAT 3 24-FEB-09 1ET8 1 VERSN REVDAT 2 01-APR-03 1ET8 1 JRNL REVDAT 1 24-AUG-00 1ET8 0 JRNL AUTH M.J.BOULANGER,M.KUKIMOTO,M.NISHIYAMA,S.HORINOUCHI,M.E.MURPHY JRNL TITL CATALYTIC ROLES FOR TWO WATER BRIDGED RESIDUES (ASP-98 AND JRNL TITL 2 HIS-255) IN THE ACTIVE SITE OF COPPER-CONTAINING NITRITE JRNL TITL 3 REDUCTASE. JRNL REF J.BIOL.CHEM. V. 275 23957 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10811642 JRNL DOI 10.1074/JBC.M001859200 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2258087.050 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 37743 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) : 0.182 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3774 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5613 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 649 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2582 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 287 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.64000 REMARK 3 B22 (A**2) : -4.64000 REMARK 3 B33 (A**2) : 9.28000 REMARK 3 B12 (A**2) : -0.84000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 50.54 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: LEAST SQUARES METHOD REMARK 4 REMARK 4 1ET8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37823 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.25900 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: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, SODIUM CACODYLATE, ZINC REMARK 280 ACETATE, PH 4.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K 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 63.82950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.85198 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.40500 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 63.82950 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 36.85198 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.40500 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 63.82950 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 36.85198 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.40500 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.70396 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 44.81000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 73.70396 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 44.81000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 73.70396 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 44.81000 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 ASSEMBLY IS A TRIMER CONSTRUCTED FROM CHAIN A REMARK 300 GENERATED BY THE THREEFOLD 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 13350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -138.0 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 ZN ZN A 504 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 GLY A 343 REMARK 465 ARG A 344 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 OD1 ASP A 79 O HOH A 840 2.12 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 ASN A 305 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 ASN A 307 N - CA - C ANGL. DEV. = -20.8 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 ALA A 137 73.20 -158.42 REMARK 500 MET A 141 29.22 -141.29 REMARK 500 GLU A 189 -15.00 -48.11 REMARK 500 LEU A 213 17.93 58.14 REMARK 500 HIS A 306 20.91 -78.22 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 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 40 OE2 REMARK 620 2 GLU A 40 OE1 53.0 REMARK 620 3 GLU A 89 OE2 84.6 136.4 REMARK 620 4 GLU A 342 OE1 116.7 75.5 142.6 REMARK 620 5 GLU A 342 OE2 89.4 93.9 95.5 57.1 REMARK 620 6 HOH A 732 O 102.5 93.2 85.9 115.8 168.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 CYS A 136 SG 135.8 REMARK 620 3 HIS A 145 ND1 102.0 103.7 REMARK 620 4 MET A 150 SD 86.3 103.3 130.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 100 NE2 REMARK 620 2 HIS A 135 NE2 110.0 REMARK 620 3 HIS A 306 NE2 107.6 108.1 REMARK 620 4 HOH A 503 O 108.1 107.4 115.6 REMARK 620 N 1 2 3 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 HOH A 625 O REMARK 620 2 HOH A 625 O 93.5 REMARK 620 3 HOH A 625 O 93.5 93.5 REMARK 620 4 HOH A 661 O 92.3 79.9 171.5 REMARK 620 5 HOH A 661 O 171.5 92.3 79.9 95.0 REMARK 620 6 HOH A 661 O 79.9 171.5 92.3 95.0 95.0 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 CU A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ET5 RELATED DB: PDB REMARK 900 1ET5 CONTAINS D98N MUTANT OF NITRITE REDUCTASE REMARK 900 RELATED ID: 1ET7 RELATED DB: PDB REMARK 900 1ET7 CONTAINS H255D MUTANT OF NITRITE REDUCTASE REMARK 900 RELATED ID: 2AFN RELATED DB: PDB REMARK 900 2AFN CONTAINS NATIVE NITRITE REDUCTASE FROM ALCALIGENES FAECALIS REMARK 900 RELATED ID: 1AS7 RELATED DB: PDB REMARK 900 1AS7 CONTAINS NATIVE OXIDIZED CRYO CRYSTAL STRUCTURE OF NITRITE REMARK 900 REDUCTASE FROM ALCALIGENES FAECALIS DBREF 1ET8 A 4 340 UNP P38501 NIR_ALCFA 40 376 SEQADV 1ET8 ASN A 255 UNP P38501 HIS 291 ENGINEERED MUTATION SEQADV 1ET8 ILE A 341 UNP P38501 CLONING ARTIFACT SEQADV 1ET8 GLU A 342 UNP P38501 CLONING ARTIFACT SEQADV 1ET8 GLY A 343 UNP P38501 CLONING ARTIFACT SEQADV 1ET8 ARG A 344 UNP P38501 CLONING ARTIFACT SEQRES 1 A 341 ALA THR ALA ALA GLU ILE ALA ALA LEU PRO ARG GLN LYS SEQRES 2 A 341 VAL GLU LEU VAL ASP PRO PRO PHE VAL HIS ALA HIS SER SEQRES 3 A 341 GLN VAL ALA GLU GLY GLY PRO LYS VAL VAL GLU PHE THR SEQRES 4 A 341 MET VAL ILE GLU GLU LYS LYS ILE VAL ILE ASP ASP ALA SEQRES 5 A 341 GLY THR GLU VAL HIS ALA MET ALA PHE ASN GLY THR VAL SEQRES 6 A 341 PRO GLY PRO LEU MET VAL VAL HIS GLN ASP ASP TYR LEU SEQRES 7 A 341 GLU LEU THR LEU ILE ASN PRO GLU THR ASN THR LEU MET SEQRES 8 A 341 HIS ASN ILE ASP PHE HIS ALA ALA THR GLY ALA LEU GLY SEQRES 9 A 341 GLY GLY GLY LEU THR GLU ILE ASN PRO GLY GLU LYS THR SEQRES 10 A 341 ILE LEU ARG PHE LYS ALA THR LYS PRO GLY VAL PHE VAL SEQRES 11 A 341 TYR HIS CYS ALA PRO PRO GLY MET VAL PRO TRP HIS VAL SEQRES 12 A 341 VAL SER GLY MET ASN GLY ALA ILE MET VAL LEU PRO ARG SEQRES 13 A 341 GLU GLY LEU HIS ASP GLY LYS GLY LYS ALA LEU THR TYR SEQRES 14 A 341 ASP LYS ILE TYR TYR VAL GLY GLU GLN ASP PHE TYR VAL SEQRES 15 A 341 PRO ARG ASP GLU ASN GLY LYS TYR LYS LYS TYR GLU ALA SEQRES 16 A 341 PRO GLY ASP ALA TYR GLU ASP THR VAL LYS VAL MET ARG SEQRES 17 A 341 THR LEU THR PRO THR HIS VAL VAL PHE ASN GLY ALA VAL SEQRES 18 A 341 GLY ALA LEU THR GLY ASP LYS ALA MET THR ALA ALA VAL SEQRES 19 A 341 GLY GLU LYS VAL LEU ILE VAL HIS SER GLN ALA ASN ARG SEQRES 20 A 341 ASP THR ARG PRO ASN LEU ILE GLY GLY HIS GLY ASP TYR SEQRES 21 A 341 VAL TRP ALA THR GLY LYS PHE ASN THR PRO PRO ASP VAL SEQRES 22 A 341 ASP GLN GLU THR TRP PHE ILE PRO GLY GLY ALA ALA GLY SEQRES 23 A 341 ALA ALA PHE TYR THR PHE GLN GLN PRO GLY ILE TYR ALA SEQRES 24 A 341 TYR VAL ASN HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY SEQRES 25 A 341 ALA ALA ALA HIS PHE LYS VAL THR GLY GLU TRP ASN ASP SEQRES 26 A 341 ASP LEU MET THR SER VAL LEU ALA PRO SER GLY THR ILE SEQRES 27 A 341 GLU GLY ARG HET CU A 501 1 HET CU A 502 1 HET ZN A 504 1 HET ZN A 505 1 HETNAM CU COPPER (II) ION HETNAM ZN ZINC ION FORMUL 2 CU 2(CU 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *287(H2 O) HELIX 1 1 THR A 5 ALA A 11 1 7 HELIX 2 2 GLY A 104 THR A 112 5 9 HELIX 3 3 MET A 141 VAL A 147 1 7 HELIX 4 4 ALA A 198 ARG A 211 1 14 HELIX 5 5 THR A 228 ALA A 232 5 5 HELIX 6 6 ASN A 307 GLU A 313 1 7 SHEET 1 A 4 GLU A 118 LYS A 125 0 SHEET 2 A 4 TYR A 80 ASN A 87 -1 N LEU A 81 O PHE A 124 SHEET 3 A 4 VAL A 38 VAL A 51 1 N VAL A 39 O TYR A 80 SHEET 4 A 4 ARG A 14 LYS A 16 1 O GLN A 15 N GLU A 40 SHEET 1 B 4 GLU A 118 LYS A 125 0 SHEET 2 B 4 TYR A 80 ASN A 87 -1 N LEU A 81 O PHE A 124 SHEET 3 B 4 VAL A 38 VAL A 51 1 N VAL A 39 O TYR A 80 SHEET 4 B 4 GLU A 58 PHE A 64 -1 N VAL A 59 O ILE A 50 SHEET 1 C 4 MET A 73 HIS A 76 0 SHEET 2 C 4 ASN A 151 LEU A 157 1 O ALA A 153 N MET A 73 SHEET 3 C 4 GLY A 130 HIS A 135 -1 O GLY A 130 N VAL A 156 SHEET 4 C 4 ASP A 98 PHE A 99 -1 N ASP A 98 O HIS A 135 SHEET 1 D 6 HIS A 217 PHE A 220 0 SHEET 2 D 6 LYS A 174 PHE A 183 -1 N GLN A 181 O VAL A 219 SHEET 3 D 6 LYS A 240 GLN A 247 1 O LYS A 240 N LYS A 174 SHEET 4 D 6 ALA A 287 THR A 294 -1 O ALA A 287 N GLN A 247 SHEET 5 D 6 GLY A 261 TRP A 265 -1 N ASP A 262 O PHE A 292 SHEET 6 D 6 ASP A 275 GLN A 278 -1 N ASP A 275 O VAL A 264 SHEET 1 E 4 MET A 233 ALA A 236 0 SHEET 2 E 4 ALA A 317 THR A 323 1 O HIS A 319 N MET A 233 SHEET 3 E 4 GLY A 299 ASN A 305 -1 N GLY A 299 O VAL A 322 SHEET 4 E 4 PRO A 254 ILE A 257 -1 O ASN A 255 N VAL A 304 LINK OE2 GLU A 40 ZN ZN A 505 8444 1555 2.35 LINK OE1 GLU A 40 ZN ZN A 505 8444 1555 2.51 LINK OE2 GLU A 89 ZN ZN A 505 1555 1555 2.13 LINK ND1 HIS A 95 CU CU A 501 1555 1555 2.11 LINK NE2 HIS A 100 CU CU A 502 1555 1555 1.98 LINK NE2 HIS A 135 CU CU A 502 1555 1555 2.13 LINK SG CYS A 136 CU CU A 501 1555 1555 2.20 LINK ND1 HIS A 145 CU CU A 501 1555 1555 1.92 LINK SD MET A 150 CU CU A 501 1555 1555 2.63 LINK NE2 HIS A 306 CU CU A 502 2555 1555 2.19 LINK OE1 GLU A 342 ZN ZN A 505 2555 1555 2.39 LINK OE2 GLU A 342 ZN ZN A 505 2555 1555 2.16 LINK CU CU A 502 O HOH A 503 1555 1555 1.76 LINK ZN ZN A 504 O HOH A 625 1555 1555 2.24 LINK ZN ZN A 504 O HOH A 625 1555 3555 2.24 LINK ZN ZN A 504 O HOH A 625 1555 2555 2.24 LINK ZN ZN A 504 O HOH A 661 1555 1555 2.07 LINK ZN ZN A 504 O HOH A 661 1555 3555 2.07 LINK ZN ZN A 504 O HOH A 661 1555 2555 2.07 LINK ZN ZN A 505 O HOH A 732 1555 1555 2.02 CISPEP 1 PRO A 22 PRO A 23 0 -0.20 CISPEP 2 VAL A 68 PRO A 69 0 -0.10 SITE 1 AC1 4 HIS A 95 CYS A 136 HIS A 145 MET A 150 SITE 1 AC2 5 ASP A 98 HIS A 100 HIS A 135 HIS A 306 SITE 2 AC2 5 HOH A 503 SITE 1 AC3 2 HOH A 625 HOH A 661 SITE 1 AC4 4 GLU A 40 GLU A 89 GLU A 342 HOH A 732 CRYST1 127.659 127.659 67.215 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 0.007833 0.004523 0.000000 0.00000 SCALE2 0.000000 0.009045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014878 0.00000