HEADER REDUCTASE 22-OCT-04 1WA2 TITLE CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE TITLE 2 REDUCTASE WITH NITRITE BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: NITRITE REDUCTASE, NIR; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES XYLOSOXIDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 VARIANT: XYLOSOXIDANS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PENIRSP-1 KEYWDS REDUCTASE, NITRITE REDUCTASE, H313Q MUTANT, NO2, DENITRIFICATION EXPDTA X-RAY DIFFRACTION AUTHOR M.L.BARRETT,R.L.HARRIS,S.V.ANTONYUK,R.W.STRANGE,M.A.HOUGH,R.R.EADY, AUTHOR 2 G.SAWERS,S.S.HASNAIN REVDAT 4 13-DEC-23 1WA2 1 LINK REVDAT 3 22-MAY-19 1WA2 1 REMARK REVDAT 2 24-FEB-09 1WA2 1 VERSN REVDAT 1 04-JAN-05 1WA2 0 JRNL AUTH M.L.BARRETT,R.L.HARRIS,S.V.ANTONYUK,M.A.HOUGH,M.J.ELLIS, JRNL AUTH 2 G.SAWERS,R.R.EADY,S.S.HASNAIN JRNL TITL INSIGHTS INTO REDOX PARTNER INTERACTIONS AND SUBSTRATE JRNL TITL 2 BINDING IN NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS: JRNL TITL 3 CRYSTAL STRUCTURES OF THE TRP138HIS AND HIS313GLN MUTANTS JRNL REF BIOCHEMISTRY V. 43 16311 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15610025 JRNL DOI 10.1021/BI048682G REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 44676 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2257 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) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3310 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 182 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2523 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.57000 REMARK 3 B22 (A**2) : 0.57000 REMARK 3 B33 (A**2) : -0.85000 REMARK 3 B12 (A**2) : 0.28000 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): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.867 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2626 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2337 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3584 ; 1.444 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5441 ; 0.945 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 333 ; 7.171 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 395 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2945 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 502 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 488 ; 0.234 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2731 ; 0.253 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1439 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.170 ; 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): 27 ; 0.155 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 139 ; 0.294 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 43 ; 0.195 ; 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 ; 0.653 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2680 ; 1.128 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 963 ; 1.718 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 904 ; 2.676 ; 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 : 1.40 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 1WA2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1290020905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.48 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44676 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1OE1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF HIS313GLN NIR WERE GROWN REMARK 280 BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 REMARK 280 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL REMARK 280 VOLUME OF RESERVOIR SOLUTION CONSISTING OF 25% PEG-MME 550, 10 REMARK 280 MM ZINC SULPHATE, 0.1M MES PH 6.5 AND SUSPENDED OVER A 500 ML REMARK 280 RESERVOIR. CRYSTALS OF BOTH MUTANTS WERE AN INTENSE BLUE COLOUR REMARK 280 AND GREW WITHIN TWO DAYS TO APPROXIMATE DIMENSIONS 0.9 X 0.6 X REMARK 280 0.1 MM IN A RHOMBOHEDRAL MORPHOLOGY. FOR HIS313GLN_NO2.-, 10MM REMARK 280 SODIUM NITRITE WAS ADDED TO THE RESERVOIR SOLUTION PRIOR TO REMARK 280 CRYSTALLISATION., PH 6.50, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K 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 44.82050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.87713 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.85633 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 44.82050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 25.87713 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.85633 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 44.82050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 25.87713 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.85633 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.75426 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 95.71267 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 51.75426 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 95.71267 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 51.75426 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 95.71267 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 APPLY THE FOLLOWING TO CHAINS: X 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 HOH X2012 LIES ON A SPECIAL POSITION. REMARK 375 HOH X2032 LIES ON A SPECIAL POSITION. REMARK 375 HOH X2048 LIES ON A SPECIAL POSITION. REMARK 375 HOH X2231 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE HIS 337 GLN, CHAIN X. REMARK 400 (RESIDUE NUMBER 313 IN COORDINATE RECORDS BELOW). 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 GLN X 1 REMARK 465 ARG X 336 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 X 5 CE NZ REMARK 470 LYS X 10 CD CE NZ REMARK 470 LYS X 27 CD CE NZ REMARK 470 LYS X 31 CE NZ REMARK 470 ASP X 48 CG OD1 OD2 REMARK 470 LYS X 104 CE NZ REMARK 470 LYS X 186 CD CE NZ REMARK 470 LYS X 217 CE NZ REMARK 470 LYS X 230 CD CE NZ REMARK 470 LYS X 315 CE NZ REMARK 470 LYS X 319 CG CD CE NZ REMARK 470 LYS X 329 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 O HOH X 2258 O HOH X 2292 2.03 REMARK 500 O HOH X 2096 O HOH X 2324 2.13 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 X 24 -103.34 -86.81 REMARK 500 ASN X 90 -167.11 -166.05 REMARK 500 ALA X 131 62.53 -152.73 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 X 300 ASN X 301 144.98 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH X2012 DISTANCE = 7.51 ANGSTROMS REMARK 525 HOH X2032 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH X2059 DISTANCE = 6.01 ANGSTROMS 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 X1340 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS X 70 ND1 REMARK 620 2 ASP X 73 OD2 111.3 REMARK 620 3 HOH X2324 O 104.1 129.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU X1337 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS X 89 ND1 REMARK 620 2 CYS X 130 SG 127.7 REMARK 620 3 HIS X 139 ND1 100.1 120.7 REMARK 620 4 MET X 144 SD 84.8 108.3 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU X1338 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS X 94 NE2 REMARK 620 2 HIS X 129 NE2 107.3 REMARK 620 3 HIS X 300 NE2 108.0 111.1 REMARK 620 4 NO2 X1341 N 125.0 96.9 107.9 REMARK 620 5 NO2 X1341 O1 150.0 98.9 74.6 35.0 REMARK 620 6 NO2 X1341 O2 88.5 115.6 122.5 36.7 66.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN X1339 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS X 165 NE2 REMARK 620 2 ASP X 167 OD1 90.9 REMARK 620 3 ASP X 167 OD2 124.2 57.9 REMARK 620 4 GLU X 195 OE2 121.3 94.1 107.1 REMARK 620 5 HOH X2323 O 112.2 148.4 90.8 91.9 REMARK 620 N 1 2 3 4 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 X1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU X1338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN X1339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN X1340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO2 X1341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X1342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES X1343 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: 1GS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H254F 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: 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: 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: 1WA1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE DBREF 1WA2 X 1 336 UNP O68601 O68601 25 360 SEQADV 1WA2 GLN X 313 UNP O68601 HIS 337 ENGINEERED MUTATION SEQRES 1 X 336 GLN ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU SEQRES 2 X 336 VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR SEQRES 3 X 336 LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE SEQRES 4 X 336 GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR SEQRES 5 X 336 LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 X 336 THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR SEQRES 7 X 336 LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL SEQRES 8 X 336 ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS SEQRES 9 X 336 LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG SEQRES 10 X 336 PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS CYS SEQRES 11 X 336 ALA PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY SEQRES 12 X 336 MET SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU SEQRES 13 X 336 LYS ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA SEQRES 14 X 336 TYR THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY SEQRES 15 X 336 PRO ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SEQRES 16 X 336 SER TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR SEQRES 17 X 336 PRO SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU SEQRES 18 X 336 THR GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR SEQRES 19 X 336 VAL LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG SEQRES 20 X 336 PRO HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU SEQRES 21 X 336 THR GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU SEQRES 22 X 336 THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU SEQRES 23 X 336 TYR THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN SEQRES 24 X 336 HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY SEQRES 25 X 336 GLN ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET SEQRES 26 X 336 LYS GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG HET CU X1337 1 HET CU X1338 1 HET ZN X1339 1 HET ZN X1340 1 HET NO2 X1341 3 HET SO4 X1342 5 HET MES X1343 12 HETNAM CU COPPER (II) ION HETNAM ZN ZINC ION HETNAM NO2 NITRITE ION HETNAM SO4 SULFATE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 CU 2(CU 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 6 NO2 N O2 1- FORMUL 7 SO4 O4 S 2- FORMUL 8 MES C6 H13 N O4 S FORMUL 9 HOH *330(H2 O) HELIX 1 1 ASP X 2 LEU X 6 5 5 HELIX 2 2 GLY X 98 THR X 106 5 9 HELIX 3 3 MET X 135 SER X 142 1 8 HELIX 4 4 THR X 192 THR X 206 1 15 HELIX 5 5 THR X 222 ALA X 226 5 5 HELIX 6 6 ASN X 301 GLU X 307 1 7 SHEET 1 XA 4 HIS X 8 LYS X 10 0 SHEET 2 XA 4 VAL X 32 VAL X 45 1 O VAL X 32 N THR X 9 SHEET 3 XA 4 TYR X 74 ASN X 81 1 O TYR X 74 N VAL X 33 SHEET 4 XA 4 GLU X 112 LYS X 119 -1 O GLU X 112 N ASN X 81 SHEET 1 XB 3 HIS X 8 LYS X 10 0 SHEET 2 XB 3 VAL X 32 VAL X 45 1 O VAL X 32 N THR X 9 SHEET 3 XB 3 THR X 52 PHE X 58 -1 O LEU X 53 N MET X 44 SHEET 1 XC 4 LEU X 67 HIS X 70 0 SHEET 2 XC 4 SER X 145 LEU X 151 1 O THR X 147 N LEU X 67 SHEET 3 XC 4 GLY X 124 HIS X 129 -1 O GLY X 124 N VAL X 150 SHEET 4 XC 4 ASP X 92 PHE X 93 -1 O ASP X 92 N HIS X 129 SHEET 1 XD 6 HIS X 211 PHE X 214 0 SHEET 2 XD 6 ARG X 168 LEU X 177 -1 O PHE X 175 N VAL X 213 SHEET 3 XD 6 THR X 234 GLN X 241 1 O LEU X 236 N TYR X 170 SHEET 4 XD 6 SER X 281 THR X 288 -1 O SER X 281 N GLN X 241 SHEET 5 XD 6 GLY X 255 TRP X 259 -1 N ASP X 256 O LEU X 286 SHEET 6 XD 6 GLN X 269 LEU X 272 -1 O GLN X 269 N VAL X 258 SHEET 1 XE 4 LEU X 227 LYS X 230 0 SHEET 2 XE 4 ALA X 311 GLU X 317 1 O GLN X 313 N LEU X 227 SHEET 3 XE 4 GLY X 293 ASN X 299 -1 O GLY X 293 N VAL X 316 SHEET 4 XE 4 PRO X 248 LEU X 250 -1 O HIS X 249 N LEU X 298 LINK ND1 HIS X 70 ZN ZN X1340 1555 1555 2.71 LINK OD2 ASP X 73 ZN ZN X1340 1555 1555 2.18 LINK ND1 HIS X 89 CU CU X1337 1555 1555 2.11 LINK NE2 HIS X 94 CU CU X1338 1555 1555 2.01 LINK NE2 HIS X 129 CU CU X1338 1555 1555 2.05 LINK SG CYS X 130 CU CU X1337 1555 1555 2.13 LINK ND1 HIS X 139 CU CU X1337 1555 1555 2.05 LINK SD MET X 144 CU CU X1337 1555 1555 2.56 LINK NE2 HIS X 165 ZN ZN X1339 1555 1555 1.88 LINK OD1 ASP X 167 ZN ZN X1339 1555 1555 2.36 LINK OD2 ASP X 167 ZN ZN X1339 1555 1555 2.01 LINK OE2 GLU X 195 ZN ZN X1339 5555 1555 2.11 LINK NE2 HIS X 300 CU CU X1338 2555 1555 2.13 LINK CU CU X1338 N NO2 X1341 1555 1555 2.41 LINK CU CU X1338 O1 NO2 X1341 1555 1555 2.42 LINK CU CU X1338 O2 NO2 X1341 1555 1555 1.86 LINK ZN ZN X1339 O HOH X2323 1555 1555 1.71 LINK ZN ZN X1340 O HOH X2324 1555 1555 2.34 CISPEP 1 PRO X 16 PRO X 17 0 5.17 CISPEP 2 MET X 62 PRO X 63 0 -6.91 SITE 1 AC1 4 HIS X 89 CYS X 130 HIS X 139 MET X 144 SITE 1 AC2 4 HIS X 94 HIS X 129 HIS X 300 NO2 X1341 SITE 1 AC3 4 HIS X 165 ASP X 167 GLU X 195 HOH X2323 SITE 1 AC4 4 HIS X 70 ASP X 73 HOH X2096 HOH X2324 SITE 1 AC5 8 ASP X 92 HIS X 94 HIS X 129 HIS X 249 SITE 2 AC5 8 ILE X 251 HIS X 300 LEU X 302 CU X1338 SITE 1 AC6 4 ASP X 47 ASP X 48 LYS X 49 HOH X2325 SITE 1 AC7 5 LEU X 164 HIS X 165 THR X 288 HOH X2328 SITE 2 AC7 5 HOH X2330 CRYST1 89.641 89.641 143.569 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 0.011156 0.006441 0.000000 0.00000 SCALE2 0.000000 0.012881 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006965 0.00000