HEADER OXIDOREDUCTASE 30-JAN-08 2VN3 TITLE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISSIMILATORY COPPER-CONTAINING NITRITE COMPND 3 REDUCTASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 25-360; COMPND 6 SYNONYM: NITRITE REDUCTASE, NIR; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS CUPREDOXIN, TYPE 1 COPPER, TYPE 2 COPPER, OXIDOREDUCTASE, KEYWDS 2 ELECTRON TRANSFER, COPPER-CONTAINING NITRITE REDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.SATO,S.J.FIRBANK,C.LI,M.J.BANFIELD,C.DENNISON REVDAT 1 23-DEC-08 2VN3 0 JRNL AUTH K.SATO,S.J.FIRBANK,C.LI,M.J.BANFIELD,C.DENNISON JRNL TITL THE IMPORTANCE OF THE LONG TYPE 1 COPPER-BINDING JRNL TITL 2 LOOP OF NITRITE REDUCTASE FOR STRUCTURE AND JRNL TITL 3 FUNCTION. JRNL REF CHEMISTRY V. 14 5820 2008 JRNL REFN ISSN 0947-6539 JRNL PMID 18491346 JRNL DOI 10.1002/CHEM.200701997 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17023 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 916 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1232 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 2717 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.04000 REMARK 3 B12 (A**2) : -0.01000 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): 0.261 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.896 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2623 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3579 ; 1.539 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 7.271 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;34.854 ;24.259 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 397 ;14.784 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.189 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 394 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2019 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1176 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1737 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 196 ; 0.146 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 89 ; 0.172 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.141 ; 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): 1712 ; 0.788 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2688 ; 1.282 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1039 ; 1.821 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 891 ; 2.711 ; 4.500 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 : BABINET MODEL WITH 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2VN3 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JAN-08. REMARK 100 THE PDBE ID CODE IS EBI-35160. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 MICROMAX 007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC BLUE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17939 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.35 REMARK 200 RESOLUTION RANGE LOW (A) : 34.10 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.4 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.90 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.3 REMARK 200 R MERGE FOR SHELL (I) : 0.32 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1OE1 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.2 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.5, 10 MM ZNSO4 REMARK 280 AND 25 % PEG-MME 550 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.72550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.82228 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.15767 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 44.72550 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 25.82228 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.15767 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 44.72550 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 25.82228 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.15767 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.64456 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 96.31533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 51.64456 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 96.31533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 51.64456 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 96.31533 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 GENERATING THE BIOMOLECULE 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 14940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.9 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 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 MET A 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 1 CG CD OE1 NE2 REMARK 470 LYS A 5 CG CD CE NZ REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 LYS A 49 NZ REMARK 470 LYS A 162 CE NZ REMARK 470 LYS A 186 CD CE NZ REMARK 470 GLN A 202 CD OE1 NE2 REMARK 470 LYS A 319 CD CE NZ REMARK 470 LYS A 329 CD CE NZ 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 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 2 111.71 4.00 REMARK 500 GLN A 24 -98.93 -83.08 REMARK 500 MET A 135 25.08 -146.67 REMARK 500 LEU A 207 19.31 55.39 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 GLN A 1 ASP A 2 -148.46 REMARK 500 HIS A 300 ASN A 301 147.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 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 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2161 O REMARK 620 2 HIS A 165 NE2 87.7 REMARK 620 3 GLU A 195 OE2 84.3 119.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 401 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 139 ND1 REMARK 620 2 CYS A 130 SG 116.2 REMARK 620 3 HIS A 89 ND1 99.1 124.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 402 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 129 NE2 REMARK 620 2 HIS A 300 NE2 108.4 REMARK 620 3 HIS A 94 NE2 103.7 107.1 REMARK 620 4 HOH A2052 O 111.3 116.3 109.2 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GS8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M144A MUTANT OF REMARK 900 ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE REMARK 900 RELATED ID: 2VM3 RELATED DB: PDB REMARK 900 STRUCTURE OF ALCALIGENES XYLOSOXIDANS IN SPACE REMARK 900 GROUP R3 - 1 OF 2 REMARK 900 RELATED ID: 1OE2 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF D92E MUTANT REMARK 900 OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE REMARK 900 RELATED ID: 1GS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H254F MUTANT OF REMARK 900 ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE REMARK 900 RELATED ID: 1WA1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H313Q MUTANT OF REMARK 900 ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE REMARK 900 RELATED ID: 2BP8 RELATED DB: PDB REMARK 900 M144Q STRUCTURE OF NITRITE REDUCTASE FROM REMARK 900 ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1OE1 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF THE WILDTYPE REMARK 900 NATIVE NITRITE REDUCTASE FROM ALCALIGENES REMARK 900 XYLOSOXIDANS REMARK 900 RELATED ID: 1WA2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H313Q MUTANT OF REMARK 900 ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE WITH REMARK 900 NITRITE BOUND REMARK 900 RELATED ID: 2BP0 RELATED DB: PDB REMARK 900 M144L MUTANT OF NITRITE REDUCTASE FROM REMARK 900 ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1HAW RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REMARK 900 REDUCTASE AT HIGH PH AND IN COPPER FREE REMARK 900 FORM AT 1.9E RESOLUTION REMARK 900 RELATED ID: 1NDT RELATED DB: PDB REMARK 900 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1WAE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H129V MUTANT OF REMARK 900 ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE REMARK 900 RELATED ID: 1OE3 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF 'HALF APO' REMARK 900 NIR REMARK 900 RELATED ID: 2JFC RELATED DB: PDB REMARK 900 M144L MUTANT OF NITRITE REDUCTASE FROM REMARK 900 ALCALIGENES XYLOSOXIDANS IN SPACE GROUP REMARK 900 P212121 REMARK 900 RELATED ID: 1GS6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M144A MUTANT OF REMARK 900 ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE REMARK 900 RELATED ID: 1HAU RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REMARK 900 REDUCTASE AT HIGH PH AND IN COPPER FREE REMARK 900 FORM AT 1.9E RESOLUTION REMARK 900 RELATED ID: 2BO0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C130A MUTANT OF REMARK 900 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1BQ5 RELATED DB: PDB REMARK 900 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 GIFU 1051 REMARK 900 RELATED ID: 2VMJ RELATED DB: PDB REMARK 900 TYPE 1 COPPER-BINDING LOOP OF NITRITE REMARK 900 REDUCTASE MUTANT: 130-CAPEGMVPWHVVSGM-144 TO REMARK 900 130-CTPHPFM-136 REMARK 900 RELATED ID: 2VM4 RELATED DB: PDB REMARK 900 STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REMARK 900 REDUCTASE IN SPACE GROUP R3 - 2 OF 2 REMARK 900 RELATED ID: 1WA0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF W138H MUTANT OF REMARK 900 ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE DBREF 2VN3 A 0 0 PDB 2VN3 2VN3 0 0 DBREF 2VN3 A 1 336 UNP O68601 O68601_ALCXX 25 360 SEQRES 1 A 337 MET GLN ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR SEQRES 2 A 337 LEU VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA SEQRES 3 A 337 THR LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR SEQRES 4 A 337 ILE GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR SEQRES 5 A 337 THR LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY SEQRES 6 A 337 PRO THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU SEQRES 7 A 337 THR LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN SEQRES 8 A 337 VAL ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA SEQRES 9 A 337 LYS LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU SEQRES 10 A 337 ARG PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS SEQRES 11 A 337 CYS ALA PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER SEQRES 12 A 337 GLY MET SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY SEQRES 13 A 337 LEU LYS ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG SEQRES 14 A 337 ALA TYR THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS SEQRES 15 A 337 GLY PRO ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA SEQRES 16 A 337 GLU SER TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU SEQRES 17 A 337 THR PRO SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA SEQRES 18 A 337 LEU THR GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU SEQRES 19 A 337 THR VAL LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR SEQRES 20 A 337 ARG PRO HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP SEQRES 21 A 337 GLU THR GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU SEQRES 22 A 337 GLU THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA SEQRES 23 A 337 LEU TYR THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU SEQRES 24 A 337 ASN HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA SEQRES 25 A 337 GLY HIS ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU SEQRES 26 A 337 MET LYS GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG HET CU A 401 1 HET CU A 402 1 HET ZN A 403 1 HET SO4 A 404 5 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETNAM CU COPPER (II) ION FORMUL 2 SO4 O4 S 2- FORMUL 3 ZN ZN 2+ FORMUL 4 CU 2(CU 2+) FORMUL 5 HOH *161(H2 O1) HELIX 1 1 ASP A 2 LEU A 6 5 5 HELIX 2 2 GLY A 98 THR A 106 5 9 HELIX 3 3 MET A 135 SER A 142 1 8 HELIX 4 4 LEU A 193 GLU A 195 5 3 HELIX 5 5 SER A 196 THR A 206 1 11 HELIX 6 6 THR A 222 ALA A 226 5 5 HELIX 7 7 ASN A 301 GLU A 307 1 7 SHEET 1 AA 4 HIS A 8 LYS A 10 0 SHEET 2 AA 4 VAL A 32 VAL A 45 1 O VAL A 32 N THR A 9 SHEET 3 AA 4 TYR A 74 ASN A 81 1 O TYR A 74 N VAL A 33 SHEET 4 AA 4 GLU A 112 LYS A 119 -1 O GLU A 112 N ASN A 81 SHEET 1 AB 3 HIS A 8 LYS A 10 0 SHEET 2 AB 3 VAL A 32 VAL A 45 1 O VAL A 32 N THR A 9 SHEET 3 AB 3 THR A 52 PHE A 58 -1 O LEU A 53 N MET A 44 SHEET 1 AC 4 LEU A 67 HIS A 70 0 SHEET 2 AC 4 SER A 145 LEU A 151 1 O THR A 147 N LEU A 67 SHEET 3 AC 4 GLY A 124 HIS A 129 -1 O GLY A 124 N VAL A 150 SHEET 4 AC 4 ASP A 92 PHE A 93 -1 O ASP A 92 N HIS A 129 SHEET 1 AD 6 HIS A 211 PHE A 214 0 SHEET 2 AD 6 ARG A 168 LEU A 177 -1 O PHE A 175 N VAL A 213 SHEET 3 AD 6 THR A 234 GLN A 241 1 O LEU A 236 N TYR A 170 SHEET 4 AD 6 SER A 281 THR A 288 -1 O SER A 281 N GLN A 241 SHEET 5 AD 6 GLY A 255 TRP A 259 -1 N ASP A 256 O LEU A 286 SHEET 6 AD 6 GLN A 269 LEU A 272 -1 O GLN A 269 N VAL A 258 SHEET 1 AE 4 LEU A 227 LYS A 230 0 SHEET 2 AE 4 ALA A 311 GLU A 317 1 O HIS A 313 N LEU A 227 SHEET 3 AE 4 GLY A 293 ASN A 299 -1 O GLY A 293 N VAL A 316 SHEET 4 AE 4 PRO A 248 ILE A 251 -1 O HIS A 249 N LEU A 298 LINK CU CU A 401 ND1 HIS A 139 1555 1555 2.00 LINK CU CU A 401 SG CYS A 130 1555 1555 2.19 LINK CU CU A 401 ND1 HIS A 89 1555 1555 2.23 LINK CU CU A 402 O HOH A2052 1555 1555 1.83 LINK CU CU A 402 NE2 HIS A 94 1555 1555 2.12 LINK CU CU A 402 NE2 HIS A 300 1555 2555 2.15 LINK CU CU A 402 NE2 HIS A 129 1555 1555 1.97 LINK ZN ZN A 403 OE2 GLU A 195 1555 5555 2.37 LINK ZN ZN A 403 NE2 HIS A 165 1555 1555 1.99 LINK ZN ZN A 403 O HOH A2161 1555 1555 1.69 CISPEP 1 PRO A 16 PRO A 17 0 5.24 CISPEP 2 MET A 62 PRO A 63 0 -1.45 SITE 1 AC1 4 HIS A 89 CYS A 130 HIS A 139 MET A 144 SITE 1 AC2 4 HIS A 94 HIS A 129 HIS A 300 HOH A2052 SITE 1 AC3 4 HIS A 165 ASP A 167 GLU A 195 HOH A2161 SITE 1 AC4 4 ALA A 3 ASP A 4 LEU A 6 HIS A 8 CRYST1 89.451 89.451 144.473 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 0.011179 0.006454 0.000000 0.00000 SCALE2 0.000000 0.012909 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006922 0.00000 MASTER 446 0 4 7 21 0 4 6 0 0 0 26 END