HEADER OXIDOREDUCTASE 28-JAN-08 2VMJ TITLE TYPE 1 COPPER-BINDING LOOP OF NITRITE REDUCTASE MUTANT: 130- TITLE 2 CAPEGMVPWHVVSGM-144 TO 130-CTPHPFM-136 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 25-154,168-360; COMPND 5 SYNONYM: NITRITE REDUCTASE, NIR, NITRITE REDUCTASE LOOP MUTANT; COMPND 6 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, ELECTRON TRANSFER, LOOP- KEYWDS 2 DIRECTED MUTAGENESIS, COPPER-CONTAINING NITRITE REDUCTASE, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.SATO,S.J.FIRBANK,C.LI,M.J.BANFIELD,C.DENNISON REVDAT 2 13-DEC-23 2VMJ 1 LINK REVDAT 1 23-DEC-08 2VMJ 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 LOOP OF JRNL TITL 2 NITRITE REDUCTASE FOR STRUCTURE AND 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 13879 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 746 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1022 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2469 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 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): 0.397 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.256 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.188 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.274 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2562 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3499 ; 1.536 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ; 7.000 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;37.444 ;24.299 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 377 ;15.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;20.521 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 385 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1974 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1061 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1662 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 154 ; 0.154 ; 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): 88 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.150 ; 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): 1663 ; 0.708 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2616 ; 1.192 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1017 ; 1.553 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 883 ; 2.366 ; 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 : 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 RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VMJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1290035099. 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 : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.33 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(III) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14625 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 37.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.19000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES PH 7.0, 5 MM ZNCL2 AND 10 REMARK 280 % PEG 6000, PH 7.5 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 44.90650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.92678 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.69967 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 44.90650 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 25.92678 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.69967 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 44.90650 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 25.92678 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.69967 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.85356 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 95.39933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 51.85356 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 95.39933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 51.85356 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 95.39933 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 14860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.4 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 465 GLN A 1 REMARK 465 ARG A 328 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 LYS A 5 CG CD CE NZ REMARK 470 LYS A 27 CD CE NZ REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 LYS A 154 CE NZ REMARK 470 LYS A 178 CE NZ REMARK 470 GLN A 194 CD OE1 NE2 REMARK 470 LYS A 222 NZ REMARK 470 LYS A 282 CE NZ REMARK 470 LYS A 307 CD CE NZ REMARK 470 GLU A 309 OE1 OE2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 LYS A 321 CD CE NZ 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 OD2 ASP A 73 O HOH A 2017 2.10 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 GLN A 24 -105.95 -80.80 REMARK 500 PRO A 30 118.40 -39.32 REMARK 500 LEU A 199 17.35 58.43 REMARK 500 PRO A 325 148.43 -37.22 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 A1328 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 129 NE2 108.1 REMARK 620 3 HIS A 292 NE2 105.3 112.4 REMARK 620 4 HOH A2088 O 114.3 111.6 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1330 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 130 SG REMARK 620 2 HIS A 133 ND1 109.5 REMARK 620 3 HOH A2090 O 89.1 78.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1329 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 157 NE2 REMARK 620 2 ASP A 159 OD2 129.2 REMARK 620 3 GLU A 187 OE2 110.9 119.9 REMARK 620 4 HOH A2089 O 102.1 81.3 86.6 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 ZN A1328 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1329 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1330 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A1331 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BQ5 RELATED DB: PDB REMARK 900 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051 REMARK 900 RELATED ID: 1GS6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1GS8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1HAU RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND REMARK 900 IN COPPER FREE FORM AT 1.9E RESOLUTION REMARK 900 RELATED ID: 1HAW RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND REMARK 900 IN COPPER FREE FORM AT 1.9E RESOLUTION REMARK 900 RELATED ID: 1NDT RELATED DB: PDB REMARK 900 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1OE3 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF 'HALF APO' NIR REMARK 900 RELATED ID: 1WA0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF W138H MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1WA2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE WITH NITRITE BOUND REMARK 900 RELATED ID: 2JFC RELATED DB: PDB REMARK 900 M144L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS IN REMARK 900 SPACE GROUP P212121 REMARK 900 RELATED ID: 2VM3 RELATED DB: PDB REMARK 900 STRUCTURE OF ALCALIGENES XYLOSOXIDANS IN SPACE GROUP R3 - 1 OF 2 REMARK 900 RELATED ID: 2VM4 RELATED DB: PDB REMARK 900 STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE REMARK 900 GROUP R3 - 2 OF 2 REMARK 900 RELATED ID: 1GS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H254F MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1OE1 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF THE WILDTYPE NATIVE NITRITE REMARK 900 REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1OE2 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF D92E MUTANT OF ALCALIGENES REMARK 900 XYLOSOXIDANS NITRITE REDUCTASE REMARK 900 RELATED ID: 1WA1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1WAE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H129V MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 2BO0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C130A MUTANT OF NITRITE REDUCTASE FROM REMARK 900 ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 2BP0 RELATED DB: PDB REMARK 900 M144L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 2BP8 RELATED DB: PDB REMARK 900 M144Q STRUCTURE OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE BELOW DESCRIBES A MUTANT, WHERE REMARK 999 130-CAPEGMVPWHVVSGM-144 HAS BEEN REPLACED WITH 130-CTPHPFM-136 DBREF 2VMJ A 0 0 PDB 2VMJ 2VMJ 0 0 DBREF 2VMJ A 1 130 UNP O68601 O68601_ALCXX 25 154 DBREF 2VMJ A 131 135 PDB 2VMJ 2VMJ 131 135 DBREF 2VMJ A 136 328 UNP O68601 O68601_ALCXX 168 360 SEQRES 1 A 329 MET GLN ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR SEQRES 2 A 329 LEU VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA SEQRES 3 A 329 THR LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR SEQRES 4 A 329 ILE GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR SEQRES 5 A 329 THR LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY SEQRES 6 A 329 PRO THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU SEQRES 7 A 329 THR LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN SEQRES 8 A 329 VAL ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA SEQRES 9 A 329 LYS LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU SEQRES 10 A 329 ARG PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS SEQRES 11 A 329 CYS THR PRO HIS PRO PHE MET SER GLY THR LEU MET VAL SEQRES 12 A 329 LEU PRO ARG ASP GLY LEU LYS ASP PRO GLN GLY LYS PRO SEQRES 13 A 329 LEU HIS TYR ASP ARG ALA TYR THR ILE GLY GLU PHE ASP SEQRES 14 A 329 LEU TYR ILE PRO LYS GLY PRO ASP GLY LYS TYR LYS ASP SEQRES 15 A 329 TYR ALA THR LEU ALA GLU SER TYR GLY ASP THR VAL GLN SEQRES 16 A 329 VAL MET ARG THR LEU THR PRO SER HIS ILE VAL PHE ASN SEQRES 17 A 329 GLY LYS VAL GLY ALA LEU THR GLY ALA ASN ALA LEU THR SEQRES 18 A 329 ALA LYS VAL GLY GLU THR VAL LEU LEU ILE HIS SER GLN SEQRES 19 A 329 ALA ASN ARG ASP THR ARG PRO HIS LEU ILE GLY GLY HIS SEQRES 20 A 329 GLY ASP TRP VAL TRP GLU THR GLY LYS PHE ALA ASN PRO SEQRES 21 A 329 PRO GLN ARG ASP LEU GLU THR TRP PHE ILE ARG GLY GLY SEQRES 22 A 329 SER ALA GLY ALA ALA LEU TYR THR PHE LYS GLN PRO GLY SEQRES 23 A 329 VAL TYR ALA TYR LEU ASN HIS ASN LEU ILE GLU ALA PHE SEQRES 24 A 329 GLU LEU GLY ALA ALA GLY HIS ILE LYS VAL GLU GLY LYS SEQRES 25 A 329 TRP ASN ASP ASP LEU MET LYS GLN ILE LYS ALA PRO ALA SEQRES 26 A 329 PRO ILE PRO ARG HET ZN A1328 1 HET ZN A1329 1 HET ZN A1330 1 HET EPE A1331 15 HETNAM ZN ZINC ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 ZN 3(ZN 2+) FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 6 HOH *90(H2 O) HELIX 1 1 GLY A 98 THR A 106 5 9 HELIX 2 2 THR A 184 THR A 198 1 15 HELIX 3 3 THR A 214 ALA A 218 5 5 HELIX 4 4 ASN A 293 GLU A 299 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 HIS A 133 LEU A 143 1 O THR A 139 N LEU A 67 SHEET 3 AC 4 GLY A 124 CYS A 130 -1 O GLY A 124 N VAL A 142 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 203 PHE A 206 0 SHEET 2 AD 6 ARG A 160 LEU A 169 -1 O PHE A 167 N VAL A 205 SHEET 3 AD 6 THR A 226 GLN A 233 1 O LEU A 228 N TYR A 162 SHEET 4 AD 6 SER A 273 THR A 280 -1 O SER A 273 N GLN A 233 SHEET 5 AD 6 GLY A 247 TRP A 251 -1 N ASP A 248 O LEU A 278 SHEET 6 AD 6 GLN A 261 LEU A 264 -1 O GLN A 261 N VAL A 250 SHEET 1 AE 4 LEU A 219 LYS A 222 0 SHEET 2 AE 4 ALA A 303 GLU A 309 1 O HIS A 305 N LEU A 219 SHEET 3 AE 4 GLY A 285 ASN A 291 -1 O GLY A 285 N VAL A 308 SHEET 4 AE 4 PRO A 240 ILE A 243 -1 O HIS A 241 N LEU A 290 LINK NE2 HIS A 94 ZN ZN A1328 1555 1555 2.15 LINK NE2 HIS A 129 ZN ZN A1328 1555 1555 2.09 LINK SG CYS A 130 ZN ZN A1330 1555 1555 2.19 LINK ND1 HIS A 133 ZN ZN A1330 1555 1555 2.38 LINK NE2 HIS A 157 ZN ZN A1329 1555 1555 1.94 LINK OD2 ASP A 159 ZN ZN A1329 1555 1555 2.22 LINK OE2 GLU A 187 ZN ZN A1329 5555 1555 1.87 LINK NE2 HIS A 292 ZN ZN A1328 2555 1555 2.16 LINK ZN ZN A1328 O HOH A2088 1555 1555 1.95 LINK ZN ZN A1329 O HOH A2089 1555 1555 1.99 LINK ZN ZN A1330 O HOH A2090 1555 1555 2.01 CISPEP 1 PRO A 16 PRO A 17 0 5.05 CISPEP 2 MET A 62 PRO A 63 0 -1.18 SITE 1 AC1 5 ASP A 92 HIS A 94 HIS A 129 HIS A 292 SITE 2 AC1 5 HOH A2088 SITE 1 AC2 4 HIS A 157 ASP A 159 GLU A 187 HOH A2089 SITE 1 AC3 5 HIS A 89 CYS A 130 HIS A 133 MET A 136 SITE 2 AC3 5 HOH A2090 SITE 1 AC4 5 ASP A 47 ASP A 48 LYS A 49 PHE A 298 SITE 2 AC4 5 GLU A 299 CRYST1 89.813 89.813 143.099 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 0.011134 0.006428 0.000000 0.00000 SCALE2 0.000000 0.012857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006988 0.00000