HEADER OXIDOREDUCTASE 19-APR-09 3H4F TITLE MET62LEU VARIANT OF NITRITE REDUCTASE FROM ALCALIGENES FAECLIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: CU-NIR; COMPND 5 EC: 1.7.2.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES FAECALIS; SOURCE 3 ORGANISM_TAXID: 511; SOURCE 4 STRAIN: S-6; SOURCE 5 GENE: NIR, NIRK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NITRITE REDUCTASE, NIR, HIGH-THROUGHPUT SCREENING, OXIDASE, COPPER, KEYWDS 2 FAD, FLAVOPROTEIN, METAL-BINDING, NITRATE ASSIMILATION, KEYWDS 3 OXIDOREDUCTASE, PERIPLASM, PYRROLIDONE CARBOXYLIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR I.S.MACPHERSON,F.I.ROSELL,M.SCOFIELD,A.G.MAUK,M.E.P.MURPHY REVDAT 4 06-SEP-23 3H4F 1 REMARK REVDAT 3 13-OCT-21 3H4F 1 REMARK SEQADV LINK REVDAT 2 16-FEB-10 3H4F 1 JRNL REVDAT 1 02-FEB-10 3H4F 0 JRNL AUTH I.S.MACPHERSON,F.I.ROSELL,M.SCOFIELD,A.G.MAUK,M.E.MURPHY JRNL TITL DIRECTED EVOLUTION OF COPPER NITRITE REDUCTASE TO A JRNL TITL 2 CHROMOGENIC REDUCTANT. JRNL REF PROTEIN ENG.DES.SEL. V. 23 137 2010 JRNL REFN ISSN 1741-0126 JRNL PMID 20083495 JRNL DOI 10.1093/PROTEIN/GZP084 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 50095 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2688 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3649 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7683 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 1092 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.80000 REMARK 3 B22 (A**2) : -1.34000 REMARK 3 B33 (A**2) : -0.47000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.275 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.219 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7898 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10773 ; 1.282 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1005 ; 6.977 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 342 ;33.598 ;24.737 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1182 ;13.686 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.203 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1185 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6129 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3975 ; 0.185 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5222 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 1096 ; 0.136 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.178 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.063 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 110 ; 0.202 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 57 ; 0.146 ; 0.200 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): 5131 ; 0.540 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8046 ; 0.889 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3157 ; 1.391 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2727 ; 2.141 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3H4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052678. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50095 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 84.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 84.52 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: REFINEMENT OF WILD-TYPE REMARK 200 STRUCTURE REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1SJM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.56600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.07250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.11150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.07250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.56600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.11150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 -0.08 77.04 REMARK 500 ALA A 137 67.47 -158.74 REMARK 500 MET A 141 28.73 -141.99 REMARK 500 PRO A 337 113.62 -31.65 REMARK 500 ASP B 78 -0.05 75.33 REMARK 500 MET B 141 23.98 -140.17 REMARK 500 LEU B 227 46.79 -104.91 REMARK 500 ASN C 65 14.82 59.18 REMARK 500 ALA C 137 73.71 -153.01 REMARK 500 LEU C 227 48.12 -94.57 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 306 ASN A 307 145.39 REMARK 500 HIS B 306 ASN B 307 147.46 REMARK 500 HIS C 306 ASN C 307 147.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH B 1363 REMARK 615 HOH B 1364 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 131.9 REMARK 620 3 HIS A 145 ND1 98.0 102.8 REMARK 620 4 MET A 150 SD 83.7 109.6 134.3 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 103.9 REMARK 620 3 HIS B 306 NE2 97.2 110.6 REMARK 620 4 HOH B2121 O 158.7 91.0 91.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU C 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 306 NE2 REMARK 620 2 HIS C 100 NE2 96.9 REMARK 620 3 HIS C 135 NE2 107.0 101.5 REMARK 620 4 HOH C1703 O 156.8 91.0 92.7 REMARK 620 5 HOH C2122 O 98.9 157.1 89.6 68.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 95 ND1 REMARK 620 2 CYS B 136 SG 129.2 REMARK 620 3 HIS B 145 ND1 96.4 104.6 REMARK 620 4 MET B 150 SD 87.9 109.1 132.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 100 NE2 REMARK 620 2 HIS B 135 NE2 107.2 REMARK 620 3 HIS C 306 NE2 96.9 110.2 REMARK 620 4 HOH C2120 O 161.9 85.8 89.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU C 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 95 ND1 REMARK 620 2 CYS C 136 SG 133.7 REMARK 620 3 HIS C 145 ND1 99.8 107.0 REMARK 620 4 MET C 150 SD 82.8 106.2 129.9 REMARK 620 N 1 2 3 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 CU B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU C 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SJM RELATED DB: PDB REMARK 900 HIGH-RESOLUTION STRUCTURE OF WILD-TYPE NITRITE REDUCTASE FROM REMARK 900 ALCALIGENES FAECALIS REMARK 900 RELATED ID: 3H4H RELATED DB: PDB DBREF 3H4F A 4 339 UNP P38501 NIR_ALCFA 40 375 DBREF 3H4F B 4 339 UNP P38501 NIR_ALCFA 40 375 DBREF 3H4F C 4 339 UNP P38501 NIR_ALCFA 40 375 SEQADV 3H4F LEU A 62 UNP P38501 MET 98 ENGINEERED MUTATION SEQADV 3H4F LEU B 62 UNP P38501 MET 98 ENGINEERED MUTATION SEQADV 3H4F LEU C 62 UNP P38501 MET 98 ENGINEERED MUTATION SEQRES 1 A 336 ALA THR ALA ALA GLU ILE ALA ALA LEU PRO ARG GLN LYS SEQRES 2 A 336 VAL GLU LEU VAL ASP PRO PRO PHE VAL HIS ALA HIS SER SEQRES 3 A 336 GLN VAL ALA GLU GLY GLY PRO LYS VAL VAL GLU PHE THR SEQRES 4 A 336 MET VAL ILE GLU GLU LYS LYS ILE VAL ILE ASP ASP ALA SEQRES 5 A 336 GLY THR GLU VAL HIS ALA LEU ALA PHE ASN GLY THR VAL SEQRES 6 A 336 PRO GLY PRO LEU MET VAL VAL HIS GLN ASP ASP TYR LEU SEQRES 7 A 336 GLU LEU THR LEU ILE ASN PRO GLU THR ASN THR LEU MET SEQRES 8 A 336 HIS ASN ILE ASP PHE HIS ALA ALA THR GLY ALA LEU GLY SEQRES 9 A 336 GLY GLY GLY LEU THR GLU ILE ASN PRO GLY GLU LYS THR SEQRES 10 A 336 ILE LEU ARG PHE LYS ALA THR LYS PRO GLY VAL PHE VAL SEQRES 11 A 336 TYR HIS CYS ALA PRO PRO GLY MET VAL PRO TRP HIS VAL SEQRES 12 A 336 VAL SER GLY MET ASN GLY ALA ILE MET VAL LEU PRO ARG SEQRES 13 A 336 GLU GLY LEU HIS ASP GLY LYS GLY LYS ALA LEU THR TYR SEQRES 14 A 336 ASP LYS ILE TYR TYR VAL GLY GLU GLN ASP PHE TYR VAL SEQRES 15 A 336 PRO ARG ASP GLU ASN GLY LYS TYR LYS LYS TYR GLU ALA SEQRES 16 A 336 PRO GLY ASP ALA TYR GLU ASP THR VAL LYS VAL MET ARG SEQRES 17 A 336 THR LEU THR PRO THR HIS VAL VAL PHE ASN GLY ALA VAL SEQRES 18 A 336 GLY ALA LEU THR GLY ASP LYS ALA MET THR ALA ALA VAL SEQRES 19 A 336 GLY GLU LYS VAL LEU ILE VAL HIS SER GLN ALA ASN ARG SEQRES 20 A 336 ASP THR ARG PRO HIS LEU ILE GLY GLY HIS GLY ASP TYR SEQRES 21 A 336 VAL TRP ALA THR GLY LYS PHE ASN THR PRO PRO ASP VAL SEQRES 22 A 336 ASP GLN GLU THR TRP PHE ILE PRO GLY GLY ALA ALA GLY SEQRES 23 A 336 ALA ALA PHE TYR THR PHE GLN GLN PRO GLY ILE TYR ALA SEQRES 24 A 336 TYR VAL ASN HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY SEQRES 25 A 336 ALA ALA ALA HIS PHE LYS VAL THR GLY GLU TRP ASN ASP SEQRES 26 A 336 ASP LEU MET THR SER VAL LEU ALA PRO SER GLY SEQRES 1 B 336 ALA THR ALA ALA GLU ILE ALA ALA LEU PRO ARG GLN LYS SEQRES 2 B 336 VAL GLU LEU VAL ASP PRO PRO PHE VAL HIS ALA HIS SER SEQRES 3 B 336 GLN VAL ALA GLU GLY GLY PRO LYS VAL VAL GLU PHE THR SEQRES 4 B 336 MET VAL ILE GLU GLU LYS LYS ILE VAL ILE ASP ASP ALA SEQRES 5 B 336 GLY THR GLU VAL HIS ALA LEU ALA PHE ASN GLY THR VAL SEQRES 6 B 336 PRO GLY PRO LEU MET VAL VAL HIS GLN ASP ASP TYR LEU SEQRES 7 B 336 GLU LEU THR LEU ILE ASN PRO GLU THR ASN THR LEU MET SEQRES 8 B 336 HIS ASN ILE ASP PHE HIS ALA ALA THR GLY ALA LEU GLY SEQRES 9 B 336 GLY GLY GLY LEU THR GLU ILE ASN PRO GLY GLU LYS THR SEQRES 10 B 336 ILE LEU ARG PHE LYS ALA THR LYS PRO GLY VAL PHE VAL SEQRES 11 B 336 TYR HIS CYS ALA PRO PRO GLY MET VAL PRO TRP HIS VAL SEQRES 12 B 336 VAL SER GLY MET ASN GLY ALA ILE MET VAL LEU PRO ARG SEQRES 13 B 336 GLU GLY LEU HIS ASP GLY LYS GLY LYS ALA LEU THR TYR SEQRES 14 B 336 ASP LYS ILE TYR TYR VAL GLY GLU GLN ASP PHE TYR VAL SEQRES 15 B 336 PRO ARG ASP GLU ASN GLY LYS TYR LYS LYS TYR GLU ALA SEQRES 16 B 336 PRO GLY ASP ALA TYR GLU ASP THR VAL LYS VAL MET ARG SEQRES 17 B 336 THR LEU THR PRO THR HIS VAL VAL PHE ASN GLY ALA VAL SEQRES 18 B 336 GLY ALA LEU THR GLY ASP LYS ALA MET THR ALA ALA VAL SEQRES 19 B 336 GLY GLU LYS VAL LEU ILE VAL HIS SER GLN ALA ASN ARG SEQRES 20 B 336 ASP THR ARG PRO HIS LEU ILE GLY GLY HIS GLY ASP TYR SEQRES 21 B 336 VAL TRP ALA THR GLY LYS PHE ASN THR PRO PRO ASP VAL SEQRES 22 B 336 ASP GLN GLU THR TRP PHE ILE PRO GLY GLY ALA ALA GLY SEQRES 23 B 336 ALA ALA PHE TYR THR PHE GLN GLN PRO GLY ILE TYR ALA SEQRES 24 B 336 TYR VAL ASN HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY SEQRES 25 B 336 ALA ALA ALA HIS PHE LYS VAL THR GLY GLU TRP ASN ASP SEQRES 26 B 336 ASP LEU MET THR SER VAL LEU ALA PRO SER GLY SEQRES 1 C 336 ALA THR ALA ALA GLU ILE ALA ALA LEU PRO ARG GLN LYS SEQRES 2 C 336 VAL GLU LEU VAL ASP PRO PRO PHE VAL HIS ALA HIS SER SEQRES 3 C 336 GLN VAL ALA GLU GLY GLY PRO LYS VAL VAL GLU PHE THR SEQRES 4 C 336 MET VAL ILE GLU GLU LYS LYS ILE VAL ILE ASP ASP ALA SEQRES 5 C 336 GLY THR GLU VAL HIS ALA LEU ALA PHE ASN GLY THR VAL SEQRES 6 C 336 PRO GLY PRO LEU MET VAL VAL HIS GLN ASP ASP TYR LEU SEQRES 7 C 336 GLU LEU THR LEU ILE ASN PRO GLU THR ASN THR LEU MET SEQRES 8 C 336 HIS ASN ILE ASP PHE HIS ALA ALA THR GLY ALA LEU GLY SEQRES 9 C 336 GLY GLY GLY LEU THR GLU ILE ASN PRO GLY GLU LYS THR SEQRES 10 C 336 ILE LEU ARG PHE LYS ALA THR LYS PRO GLY VAL PHE VAL SEQRES 11 C 336 TYR HIS CYS ALA PRO PRO GLY MET VAL PRO TRP HIS VAL SEQRES 12 C 336 VAL SER GLY MET ASN GLY ALA ILE MET VAL LEU PRO ARG SEQRES 13 C 336 GLU GLY LEU HIS ASP GLY LYS GLY LYS ALA LEU THR TYR SEQRES 14 C 336 ASP LYS ILE TYR TYR VAL GLY GLU GLN ASP PHE TYR VAL SEQRES 15 C 336 PRO ARG ASP GLU ASN GLY LYS TYR LYS LYS TYR GLU ALA SEQRES 16 C 336 PRO GLY ASP ALA TYR GLU ASP THR VAL LYS VAL MET ARG SEQRES 17 C 336 THR LEU THR PRO THR HIS VAL VAL PHE ASN GLY ALA VAL SEQRES 18 C 336 GLY ALA LEU THR GLY ASP LYS ALA MET THR ALA ALA VAL SEQRES 19 C 336 GLY GLU LYS VAL LEU ILE VAL HIS SER GLN ALA ASN ARG SEQRES 20 C 336 ASP THR ARG PRO HIS LEU ILE GLY GLY HIS GLY ASP TYR SEQRES 21 C 336 VAL TRP ALA THR GLY LYS PHE ASN THR PRO PRO ASP VAL SEQRES 22 C 336 ASP GLN GLU THR TRP PHE ILE PRO GLY GLY ALA ALA GLY SEQRES 23 C 336 ALA ALA PHE TYR THR PHE GLN GLN PRO GLY ILE TYR ALA SEQRES 24 C 336 TYR VAL ASN HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY SEQRES 25 C 336 ALA ALA ALA HIS PHE LYS VAL THR GLY GLU TRP ASN ASP SEQRES 26 C 336 ASP LEU MET THR SER VAL LEU ALA PRO SER GLY HET CU A 501 1 HET CU A 502 1 HET CU B 501 1 HET CU B 502 1 HET CU C 501 1 HET CU C 502 1 HETNAM CU COPPER (II) ION FORMUL 4 CU 6(CU 2+) FORMUL 10 HOH *1092(H2 O) HELIX 1 1 THR A 5 LEU A 12 1 8 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 ASP A 201 5 4 HELIX 5 5 ALA A 202 THR A 212 1 11 HELIX 6 6 THR A 228 ALA A 232 5 5 HELIX 7 7 ASN A 307 GLU A 313 1 7 HELIX 8 8 THR B 5 LEU B 12 1 8 HELIX 9 9 GLY B 104 THR B 112 5 9 HELIX 10 10 MET B 141 SER B 148 1 8 HELIX 11 11 PRO B 199 ASP B 201 5 3 HELIX 12 12 ALA B 202 THR B 212 1 11 HELIX 13 13 THR B 228 ALA B 232 5 5 HELIX 14 14 ASN B 307 GLU B 313 1 7 HELIX 15 15 THR C 5 ALA C 11 1 7 HELIX 16 16 GLY C 104 GLY C 109 5 6 HELIX 17 17 MET C 141 VAL C 147 1 7 HELIX 18 18 ALA C 198 ARG C 211 1 14 HELIX 19 19 THR C 228 ALA C 232 5 5 HELIX 20 20 ASN C 307 GLU C 313 1 7 SHEET 1 A 3 ARG A 14 LYS A 16 0 SHEET 2 A 3 VAL A 38 VAL A 51 1 O GLU A 40 N GLN A 15 SHEET 3 A 3 GLU A 58 PHE A 64 -1 O ALA A 63 N GLU A 46 SHEET 1 B 5 ARG A 14 LYS A 16 0 SHEET 2 B 5 VAL A 38 VAL A 51 1 O GLU A 40 N GLN A 15 SHEET 3 B 5 TYR A 80 ASN A 87 1 O GLU A 82 N VAL A 39 SHEET 4 B 5 GLU A 118 LYS A 125 -1 O GLU A 118 N ASN A 87 SHEET 5 B 5 MET B 331 SER B 338 -1 O SER B 338 N LYS A 119 SHEET 1 C 4 MET A 73 HIS A 76 0 SHEET 2 C 4 ASN A 151 LEU A 157 1 O MET A 155 N MET A 73 SHEET 3 C 4 GLY A 130 HIS A 135 -1 N GLY A 130 O 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 2 LEU A 162 HIS A 163 0 SHEET 2 D 2 ALA A 169 LEU A 170 -1 O LEU A 170 N 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 VAL A 244 N VAL A 178 SHEET 4 E 6 ALA A 287 THR A 294 -1 O ALA A 291 N ILE A 243 SHEET 5 E 6 GLY A 261 TRP A 265 -1 N TYR A 263 O PHE A 292 SHEET 6 E 6 ASP A 275 GLN A 278 -1 O ASP A 275 N 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 LYS A 321 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 N ILE A 257 O ALA A 302 SHEET 1 G 5 MET A 331 SER A 338 0 SHEET 2 G 5 GLU C 118 LYS C 125 -1 O ARG C 123 N THR A 332 SHEET 3 G 5 TYR C 80 ASN C 87 -1 N LEU C 81 O PHE C 124 SHEET 4 G 5 VAL C 38 VAL C 51 1 N VAL C 39 O TYR C 80 SHEET 5 G 5 ARG C 14 LYS C 16 1 N GLN C 15 O GLU C 40 SHEET 1 H 5 MET A 331 SER A 338 0 SHEET 2 H 5 GLU C 118 LYS C 125 -1 O ARG C 123 N THR A 332 SHEET 3 H 5 TYR C 80 ASN C 87 -1 N LEU C 81 O PHE C 124 SHEET 4 H 5 VAL C 38 VAL C 51 1 N VAL C 39 O TYR C 80 SHEET 5 H 5 GLU C 58 PHE C 64 -1 O ALA C 63 N GLU C 46 SHEET 1 I 3 ARG B 14 LYS B 16 0 SHEET 2 I 3 VAL B 38 VAL B 51 1 O GLU B 40 N GLN B 15 SHEET 3 I 3 GLU B 58 PHE B 64 -1 O VAL B 59 N ILE B 50 SHEET 1 J 5 ARG B 14 LYS B 16 0 SHEET 2 J 5 VAL B 38 VAL B 51 1 O GLU B 40 N GLN B 15 SHEET 3 J 5 TYR B 80 ASN B 87 1 O TYR B 80 N VAL B 39 SHEET 4 J 5 GLU B 118 LYS B 125 -1 O GLU B 118 N ASN B 87 SHEET 5 J 5 MET C 331 SER C 338 -1 O SER C 338 N LYS B 119 SHEET 1 K 4 MET B 73 HIS B 76 0 SHEET 2 K 4 ASN B 151 LEU B 157 1 O MET B 155 N MET B 73 SHEET 3 K 4 GLY B 130 HIS B 135 -1 N GLY B 130 O VAL B 156 SHEET 4 K 4 ASP B 98 PHE B 99 -1 N ASP B 98 O HIS B 135 SHEET 1 L 6 HIS B 217 PHE B 220 0 SHEET 2 L 6 LYS B 174 PHE B 183 -1 N GLN B 181 O VAL B 219 SHEET 3 L 6 LYS B 240 GLN B 247 1 O VAL B 244 N VAL B 178 SHEET 4 L 6 ALA B 287 THR B 294 -1 O ALA B 291 N ILE B 243 SHEET 5 L 6 GLY B 261 TRP B 265 -1 N TYR B 263 O PHE B 292 SHEET 6 L 6 ASP B 275 GLN B 278 -1 O ASP B 275 N VAL B 264 SHEET 1 M 4 MET B 233 ALA B 236 0 SHEET 2 M 4 ALA B 317 THR B 323 1 O LYS B 321 N MET B 233 SHEET 3 M 4 GLY B 299 ASN B 305 -1 N TYR B 303 O ALA B 318 SHEET 4 M 4 PRO B 254 ILE B 257 -1 N ILE B 257 O ALA B 302 SHEET 1 N 4 MET C 73 HIS C 76 0 SHEET 2 N 4 ASN C 151 LEU C 157 1 O MET C 155 N MET C 73 SHEET 3 N 4 GLY C 130 HIS C 135 -1 N GLY C 130 O VAL C 156 SHEET 4 N 4 ASP C 98 PHE C 99 -1 N ASP C 98 O HIS C 135 SHEET 1 O 2 LEU C 162 HIS C 163 0 SHEET 2 O 2 ALA C 169 LEU C 170 -1 O LEU C 170 N LEU C 162 SHEET 1 P 6 HIS C 217 PHE C 220 0 SHEET 2 P 6 LYS C 174 PHE C 183 -1 N GLN C 181 O VAL C 219 SHEET 3 P 6 LYS C 240 GLN C 247 1 O VAL C 244 N VAL C 178 SHEET 4 P 6 ALA C 287 THR C 294 -1 O ALA C 291 N ILE C 243 SHEET 5 P 6 GLY C 261 TRP C 265 -1 N TYR C 263 O PHE C 292 SHEET 6 P 6 ASP C 275 GLN C 278 -1 O ASP C 275 N VAL C 264 SHEET 1 Q 4 MET C 233 ALA C 236 0 SHEET 2 Q 4 ALA C 317 THR C 323 1 O LYS C 321 N MET C 233 SHEET 3 Q 4 GLY C 299 ASN C 305 -1 N TYR C 303 O ALA C 318 SHEET 4 Q 4 PRO C 254 ILE C 257 -1 N ILE C 257 O ALA C 302 LINK ND1 HIS A 95 CU CU A 501 1555 1555 2.21 LINK NE2 HIS A 100 CU CU A 502 1555 1555 2.04 LINK NE2 HIS A 135 CU CU A 502 1555 1555 2.15 LINK SG CYS A 136 CU CU A 501 1555 1555 2.14 LINK ND1 HIS A 145 CU CU A 501 1555 1555 2.09 LINK SD MET A 150 CU CU A 501 1555 1555 2.39 LINK NE2 HIS A 306 CU CU C 502 1555 1555 2.11 LINK CU CU A 502 NE2 HIS B 306 1555 1555 2.09 LINK CU CU A 502 O HOH B2121 1555 1555 2.24 LINK ND1 HIS B 95 CU CU B 501 1555 1555 2.08 LINK NE2 HIS B 100 CU CU B 502 1555 1555 2.04 LINK NE2 HIS B 135 CU CU B 502 1555 1555 2.21 LINK SG CYS B 136 CU CU B 501 1555 1555 2.15 LINK ND1 HIS B 145 CU CU B 501 1555 1555 2.10 LINK SD MET B 150 CU CU B 501 1555 1555 2.49 LINK CU CU B 502 NE2 HIS C 306 1555 1555 2.02 LINK CU CU B 502 O HOH C2120 1555 1555 2.30 LINK ND1 HIS C 95 CU CU C 501 1555 1555 2.25 LINK NE2 HIS C 100 CU CU C 502 1555 1555 2.11 LINK NE2 HIS C 135 CU CU C 502 1555 1555 2.04 LINK SG CYS C 136 CU CU C 501 1555 1555 2.21 LINK ND1 HIS C 145 CU CU C 501 1555 1555 1.97 LINK SD MET C 150 CU CU C 501 1555 1555 2.49 LINK CU CU C 502 O HOH C1703 1555 1555 2.19 LINK CU CU C 502 O HOH C2122 1555 1555 2.17 CISPEP 1 PRO A 22 PRO A 23 0 6.11 CISPEP 2 VAL A 68 PRO A 69 0 2.39 CISPEP 3 PRO B 22 PRO B 23 0 8.38 CISPEP 4 VAL B 68 PRO B 69 0 -1.62 CISPEP 5 PRO C 22 PRO C 23 0 5.84 CISPEP 6 VAL C 68 PRO C 69 0 4.24 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 B 306 HOH B2121 SITE 1 AC3 4 HIS B 95 CYS B 136 HIS B 145 MET B 150 SITE 1 AC4 4 HIS B 100 HIS B 135 HIS C 306 HOH C2120 SITE 1 AC5 4 HIS C 95 CYS C 136 HIS C 145 MET C 150 SITE 1 AC6 5 HIS A 306 HIS C 100 HIS C 135 HOH C1703 SITE 2 AC6 5 HOH C2122 CRYST1 61.132 102.223 146.145 90.00 90.00 90.00 P 21 21 21 12 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 0.016358 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009783 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006843 0.00000