HEADER OXIDOREDUCTASE 12-APR-00 1ET5 TITLE CRYSTAL STRUCTURE OF NITRITE REDUCTASE ASP98ASN MUTANT FROM TITLE 2 ALCALIGENES FAECALIS S-6 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 1ET5 1 REMARK REVDAT 5 03-NOV-21 1ET5 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1ET5 1 VERSN REVDAT 3 24-FEB-09 1ET5 1 VERSN REVDAT 2 01-APR-03 1ET5 1 JRNL REVDAT 1 24-AUG-00 1ET5 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2222100.890 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 30434 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) : 0.185 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2763 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4600 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 495 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2560 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.01000 REMARK 3 B22 (A**2) : -5.01000 REMARK 3 B33 (A**2) : 10.03000 REMARK 3 B12 (A**2) : -1.89000 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) : 0.19 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) : 0.22 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) : 26.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 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 : 0.31 REMARK 3 BSOL : 59.54 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 1ET5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-98 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 : 30437 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : NULL REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.24600 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, ZINC ACETATE, PEG REMARK 280 4000, PH 4.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 63.97000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.93310 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.14200 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 63.97000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 36.93310 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.14200 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 63.97000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 36.93310 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.14200 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.86619 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 44.28400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 73.86619 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 44.28400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 73.86619 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 44.28400 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 REMARK 300 CONSTRUCTED FROM CHAIN A 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: 12710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 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 375 ZN ZN A 505 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 THR A 340 REMARK 465 ILE A 341 REMARK 465 GLU A 342 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 511 2.08 REMARK 500 ND1 HIS A 76 O HOH A 511 2.18 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 307 N - CA - C ANGL. DEV. = -20.5 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 ASP A 78 -0.34 80.18 REMARK 500 ALA A 137 71.49 -160.11 REMARK 500 ASP A 188 -175.43 -69.16 REMARK 500 HIS A 306 20.14 -78.09 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 CU A 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 CYS A 136 SG 135.1 REMARK 620 3 HIS A 145 ND1 100.4 101.3 REMARK 620 4 MET A 150 SD 86.7 106.8 131.4 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 106.8 REMARK 620 3 HIS A 306 NE2 104.0 111.7 REMARK 620 4 HOH A 503 O 113.8 113.7 106.5 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 524 O REMARK 620 2 HOH A 524 O 87.8 REMARK 620 3 HOH A 524 O 87.8 87.8 REMARK 620 4 HOH A 533 O 81.1 162.3 105.3 REMARK 620 5 HOH A 533 O 105.3 81.1 162.3 88.7 REMARK 620 6 HOH A 533 O 162.3 105.3 81.1 88.7 88.7 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 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: 1ET7 RELATED DB: PDB REMARK 900 1ET7 CONTAINS H255D MUTANT OF NITRITE REDUCTASE REMARK 900 RELATED ID: 1ET8 RELATED DB: PDB REMARK 900 1ET8 CONTAINS H255N MUTANT OF NITRITE REDUCTASE REMARK 900 RELATED ID: 2AFN RELATED DB: PDB REMARK 900 2AFN CONTAINS NATIVE NITRITE REDUCTASE FROM ALACALIGENES FAECALIS S- REMARK 900 6 REMARK 900 RELATED ID: 1AS7 RELATED DB: PDB REMARK 900 1AS7 CONTAINS OXIDIZED CRYO NATIVE NITRITE REDUCTASE FROM REMARK 900 ALCALIGENES FAECALIS S-6 DBREF 1ET5 A 4 340 UNP P38501 NIR_ALCFA 40 376 SEQADV 1ET5 ASN A 98 UNP P38501 ASP 134 ENGINEERED MUTATION SEQADV 1ET5 ILE A 341 UNP P38501 CLONING ARTIFACT SEQADV 1ET5 GLU A 342 UNP P38501 CLONING ARTIFACT SEQADV 1ET5 GLY A 343 UNP P38501 CLONING ARTIFACT SEQADV 1ET5 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 ASN 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 HIS 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 *268(H2 O) HELIX 1 1 THR A 5 LEU A 12 1 8 HELIX 2 2 GLY A 104 GLY A 109 5 6 HELIX 3 3 GLY A 108 THR A 112 5 5 HELIX 4 4 MET A 141 VAL A 147 1 7 HELIX 5 5 ALA A 198 ARG A 211 1 14 HELIX 6 6 THR A 228 ALA A 232 5 5 HELIX 7 7 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 O VAL A 39 N GLU A 82 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 O VAL A 39 N GLU A 82 SHEET 4 B 4 GLU A 58 PHE A 64 -1 O VAL A 59 N 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 ASN A 98 PHE A 99 -1 N ASN A 98 O HIS A 135 SHEET 1 D 2 LEU A 162 HIS A 163 0 SHEET 2 D 2 ALA A 169 LEU A 170 -1 N LEU A 170 O LEU A 162 SHEET 1 E 6 HIS A 217 PHE A 220 0 SHEET 2 E 6 LYS A 174 PHE A 183 -1 N GLN A 181 O VAL A 219 SHEET 3 E 6 LYS A 240 GLN A 247 1 O LYS A 240 N LYS A 174 SHEET 4 E 6 ALA A 287 THR A 294 -1 O ALA A 287 N GLN A 247 SHEET 5 E 6 GLY A 261 TRP A 265 -1 N ASP A 262 O PHE A 292 SHEET 6 E 6 ASP A 275 GLN A 278 -1 N ASP A 275 O VAL A 264 SHEET 1 F 4 MET A 233 ALA A 236 0 SHEET 2 F 4 ALA A 317 THR A 323 1 O HIS A 319 N MET A 233 SHEET 3 F 4 GLY A 299 ASN A 305 -1 N GLY A 299 O VAL A 322 SHEET 4 F 4 PRO A 254 ILE A 257 -1 O HIS A 255 N VAL A 304 LINK ND1 HIS A 95 CU CU A 501 1555 1555 2.07 LINK NE2 HIS A 100 CU CU A 502 1555 1555 1.99 LINK NE2 HIS A 135 CU CU A 502 1555 1555 2.11 LINK SG CYS A 136 CU CU A 501 1555 1555 2.20 LINK ND1 HIS A 145 CU CU A 501 1555 1555 2.02 LINK SD MET A 150 CU CU A 501 1555 1555 2.49 LINK NE2 HIS A 306 CU CU A 502 3555 1555 2.16 LINK CU CU A 502 O HOH A 503 1555 1555 2.21 LINK ZN ZN A 504 O HOH A 524 1555 1555 2.31 LINK ZN ZN A 504 O HOH A 524 1555 2555 2.31 LINK ZN ZN A 504 O HOH A 524 1555 3555 2.31 LINK ZN ZN A 504 O HOH A 533 1555 1555 2.40 LINK ZN ZN A 504 O HOH A 533 1555 2555 2.40 LINK ZN ZN A 504 O HOH A 533 1555 3555 2.40 CISPEP 1 PRO A 22 PRO A 23 0 1.28 CISPEP 2 VAL A 68 PRO A 69 0 0.15 SITE 1 AC1 4 HIS A 95 CYS A 136 HIS A 145 MET A 150 SITE 1 AC2 4 HIS A 100 HIS A 135 HIS A 306 HOH A 503 SITE 1 AC3 2 HOH A 524 HOH A 533 SITE 1 AC4 1 ASP A 251 CRYST1 127.940 127.940 66.426 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 0.007816 0.004513 0.000000 0.00000 SCALE2 0.000000 0.009025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015054 0.00000