HEADER OXIDOREDUCTASE 06-APR-05 2BO0 TITLE CRYSTAL STRUCTURE OF THE C130A MUTANT OF NITRITE REDUCTASE FROM TITLE 2 ALCALIGENES XYLOSOXIDANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NITRITE REDUCTASE, NIR; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER XYLOSOXIDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DENITRIFICATION, NITRITE REDUCTASE, C130A, MUTANT, ELECTRON TRANSFER, KEYWDS 2 OXIDOREDUCTASE, COPPER, FAD, FLAVOPROTEIN, METAL- BINDING, NITRATE KEYWDS 3 ASSIMILATION, PERIPLASMIC EXPDTA X-RAY DIFFRACTION AUTHOR M.A.HOUGH,M.J.ELLIS,S.ANTONYUK,R.W.STRANGE,G.SAWERS,R.R.EADY, AUTHOR 2 S.S.HASNAIN REVDAT 4 13-DEC-23 2BO0 1 REMARK LINK REVDAT 3 11-MAR-20 2BO0 1 REMARK SEQRES LINK ATOM REVDAT 2 24-FEB-09 2BO0 1 VERSN REVDAT 1 18-OCT-06 2BO0 0 JRNL AUTH M.A.HOUGH,M.J.ELLIS,S.ANTONYUK,R.W.STRANGE,G.SAWERS, JRNL AUTH 2 R.R.EADY,S.S.HASNAIN JRNL TITL HIGH RESOLUTION STRUCTURAL STUDIES OF MUTANTS PROVIDE JRNL TITL 2 INSIGHTS INTO CATALYSIS AND ELECTRON TRANSFER PROCESSES IN JRNL TITL 3 COPPER NITRITE REDUCTASE JRNL REF J.MOL.BIOL. V. 350 300 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15927201 JRNL DOI 10.1016/J.JMB.2005.04.006 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.108 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.113 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 1 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2573 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 492 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 1.010 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BO0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290023541. 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 : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74824 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 1NDT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 550 MME, ZNSO4, MES PH 6.5, PH REMARK 280 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.68350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.68350 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.68350 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: 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 39.52400 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 68.45758 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 79.04800 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 A2407 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 CATALYTIC ACTIVITY REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 130 TO ALA REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ARG A 336 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 5 CE NZ REMARK 480 LYS A 10 CD CE NZ REMARK 480 LYS A 27 CE NZ REMARK 480 LYS A 162 NZ REMARK 480 ASN A 225 ND2 REMARK 480 LYS A 230 CE NZ REMARK 480 LYS A 315 NZ REMARK 480 LYS A 319 CE NZ REMARK 480 LYS A 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 HD1 HIS A 239 HH TYR A 297 1.24 REMARK 500 HZ3 LYS A 319 O HOH A 2446 1.56 REMARK 500 HH TYR A 197 O HOH A 2340 1.59 REMARK 500 H ARG A 336 O HOH A 2477 1.59 REMARK 500 OD1 ASP A 323 O HOH A 2455 1.97 REMARK 500 OD1 ASP A 199 O HOH A 2345 2.00 REMARK 500 OD2 ASP A 323 O HOH A 2456 2.15 REMARK 500 NH1 ARG A 168 OE2 GLU A 233 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 184 HE3 LYS A 319 6555 1.59 REMARK 500 O HOH A 2349 O HOH A 2360 3665 2.12 REMARK 500 O HOH A 2345 O HOH A 2456 6555 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 4 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 153 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 154 N - CA - CB ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG A 168 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 168 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 TYR A 197 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 TYR A 197 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 244 NH1 - CZ - NH2 ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 244 NE - CZ - NH1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 244 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 336 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 24 -97.68 -88.14 REMARK 500 ALA A 131 57.42 -154.05 REMARK 500 MET A 135 38.28 -144.85 REMARK 500 LEU A 221 47.80 -105.97 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 300 ASN A 301 145.42 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 A2066 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A2075 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A2081 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A2166 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A2174 DISTANCE = 6.54 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 A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 8 NE2 REMARK 620 2 HOH A2483 O 178.5 REMARK 620 3 HOH A2484 O 94.6 86.8 REMARK 620 4 HOH A2485 O 97.0 82.6 89.3 REMARK 620 5 HOH A2486 O 96.0 82.6 166.8 97.1 REMARK 620 6 HOH A2487 O 92.4 88.1 84.0 168.8 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 129 NE2 108.7 REMARK 620 3 HIS A 300 NE2 102.7 108.6 REMARK 620 4 HOH A2479 O 108.3 111.3 116.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 165 NE2 REMARK 620 2 ASP A 167 OD1 86.2 REMARK 620 3 ASP A 167 OD2 106.0 52.9 REMARK 620 4 HOH A2480 O 103.5 149.9 97.0 REMARK 620 5 HOH A2481 O 96.5 110.9 150.2 96.4 REMARK 620 6 HOH A2482 O 128.7 83.9 107.4 109.8 42.9 REMARK 620 N 1 2 3 4 5 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 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A1340 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 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: 1WAE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H129V MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE DBREF 2BO0 A 1 336 UNP O68601 O68601_ALCXX 25 360 SEQADV 2BO0 ALA A 130 UNP O68601 CYS 154 ENGINEERED MUTATION SEQRES 1 A 336 PCA ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU SEQRES 2 A 336 VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR SEQRES 3 A 336 LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE SEQRES 4 A 336 GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR SEQRES 5 A 336 LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 A 336 THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR SEQRES 7 A 336 LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL SEQRES 8 A 336 ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS SEQRES 9 A 336 LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG SEQRES 10 A 336 PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS ALA SEQRES 11 A 336 ALA PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY SEQRES 12 A 336 MET SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU SEQRES 13 A 336 LYS ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA SEQRES 14 A 336 TYR THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY SEQRES 15 A 336 PRO ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SEQRES 16 A 336 SER TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR SEQRES 17 A 336 PRO SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU SEQRES 18 A 336 THR GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR SEQRES 19 A 336 VAL LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG SEQRES 20 A 336 PRO HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU SEQRES 21 A 336 THR GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU SEQRES 22 A 336 THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU SEQRES 23 A 336 TYR THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN SEQRES 24 A 336 HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY SEQRES 25 A 336 HIS ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET SEQRES 26 A 336 LYS GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG MODRES 2BO0 PCA A 1 GLU PYROGLUTAMIC ACID HET PCA A 1 8 HET ZN A 502 1 HET ZN A 504 1 HET ZN A 505 1 HET PG4 A1340 13 HETNAM PCA PYROGLUTAMIC ACID HETNAM ZN ZINC ION HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 1 PCA C5 H7 N O3 FORMUL 2 ZN 3(ZN 2+) FORMUL 5 PG4 C8 H18 O5 FORMUL 6 HOH *492(H2 O) 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 THR A 192 THR A 206 1 15 HELIX 5 5 THR A 222 ALA A 226 5 5 HELIX 6 6 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 LEU A 250 -1 O HIS A 249 N LEU A 298 LINK C PCA A 1 N ASP A 2 1555 1555 1.33 LINK NE2 HIS A 8 ZN ZN A 505 1555 1555 2.07 LINK NE2 HIS A 94 ZN ZN A 502 1555 1555 2.02 LINK NE2 HIS A 129 ZN ZN A 502 1555 1555 2.02 LINK NE2 HIS A 165 ZN ZN A 504 1555 1555 2.06 LINK OD1 ASP A 167 ZN ZN A 504 1555 1555 2.76 LINK OD2 ASP A 167 ZN ZN A 504 1555 1555 2.02 LINK NE2 HIS A 300 ZN ZN A 502 3665 1555 1.98 LINK ZN ZN A 502 O HOH A2479 1555 1555 1.93 LINK ZN ZN A 504 O HOH A2480 1555 1555 2.01 LINK ZN ZN A 504 O HOH A2481 1555 1555 2.30 LINK ZN ZN A 504 O HOH A2482 1555 1555 1.85 LINK ZN ZN A 505 O HOH A2483 1555 1555 2.19 LINK ZN ZN A 505 O HOH A2484 1555 1555 2.19 LINK ZN ZN A 505 O HOH A2485 1555 1555 2.18 LINK ZN ZN A 505 O HOH A2486 1555 1555 2.12 LINK ZN ZN A 505 O HOH A2487 1555 1555 2.01 CISPEP 1 PRO A 16 PRO A 17 0 6.56 CISPEP 2 MET A 62 PRO A 63 0 -8.12 SITE 1 AC1 5 ASP A 92 HIS A 94 HIS A 129 HIS A 300 SITE 2 AC1 5 HOH A2479 SITE 1 AC2 5 HIS A 165 ASP A 167 HOH A2480 HOH A2481 SITE 2 AC2 5 HOH A2482 SITE 1 AC3 6 HIS A 8 HOH A2483 HOH A2484 HOH A2485 SITE 2 AC3 6 HOH A2486 HOH A2487 SITE 1 AC4 8 VAL A 294 ALA A 296 PHE A 306 HIS A 313 SITE 2 AC4 8 HOH A2489 HOH A2490 HOH A2491 HOH A2492 CRYST1 79.048 79.048 99.367 90.00 90.00 120.00 P 63 6 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 0.012651 0.007304 0.000000 0.00000 SCALE2 0.000000 0.014608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010064 0.00000 HETATM 1 N PCA A 1 13.342 37.680 -22.435 0.63 26.28 N ANISOU 1 N PCA A 1 3648 2844 3495 -527 620 372 N HETATM 2 CA PCA A 1 11.955 37.897 -22.122 1.00 28.54 C ANISOU 2 CA PCA A 1 3959 3013 3869 -408 1318 379 C HETATM 3 CB PCA A 1 11.389 36.469 -22.161 0.63 30.72 C ANISOU 3 CB PCA A 1 3977 3319 4374 -812 1281 203 C HETATM 4 CG PCA A 1 12.605 35.526 -21.963 0.63 29.51 C ANISOU 4 CG PCA A 1 4364 2780 4070 -669 1529 -43 C HETATM 5 CD PCA A 1 13.727 36.397 -22.430 0.63 28.12 C ANISOU 5 CD PCA A 1 4066 2882 3737 -464 1484 63 C HETATM 6 OE PCA A 1 14.833 36.036 -22.754 0.63 25.50 O ANISOU 6 OE PCA A 1 3712 3732 2245 173 597 1359 O HETATM 7 C PCA A 1 11.701 38.585 -20.816 1.00 27.96 C ANISOU 7 C PCA A 1 3355 3607 3664 363 41 119 C HETATM 8 O PCA A 1 12.346 38.338 -19.815 1.00 35.16 O ANISOU 8 O PCA A 1 2874 6084 4402 533 -438 180 O