HEADER OXIDOREDUCTASE 16-AUG-06 2DWS TITLE CU-CONTAINING NITRITE REDUCTASE AT PH 8.4 WITH BOUND NITRITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CU-NIR; COMPND 5 EC: 1.7.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER SPHAEROIDES; SOURCE 3 ORGANISM_TAXID: 1063; SOURCE 4 STRAIN: 2.4.3; SOURCE 5 GENE: NIRK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS COPPER PROTEIN, CUPREDOXIN, DENITRIFICATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.JACOBSON REVDAT 7 25-OCT-23 2DWS 1 REMARK LINK REVDAT 6 11-OCT-17 2DWS 1 REMARK REVDAT 5 13-JUL-11 2DWS 1 VERSN REVDAT 4 24-FEB-09 2DWS 1 VERSN REVDAT 3 13-MAR-07 2DWS 1 JRNL REVDAT 2 12-DEC-06 2DWS 1 JRNL REVDAT 1 05-DEC-06 2DWS 0 JRNL AUTH F.JACOBSON,A.PISTORIUS,D.FARKAS,W.DE GRIP,O.HANSSON, JRNL AUTH 2 L.SJOLIN,R.NEUTZE JRNL TITL PH DEPENDENCE OF COPPER GEOMETRY, REDUCTION POTENTIAL, AND JRNL TITL 2 NITRITE AFFINITY IN NITRITE REDUCTASE JRNL REF J.BIOL.CHEM. V. 282 6347 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17148448 JRNL DOI 10.1074/JBC.M605746200 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : -1 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : -1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 31708 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : 5.0 PERCENT, RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1585 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2522 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL 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): NULL ; 0.013 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.575 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DWS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000025939. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.996 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31708 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 26.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 1ZV2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, MGCL2, NANO2, PEG 4000, PH 8.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 41.10200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.73025 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.71733 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 41.10200 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 23.73025 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.71733 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 41.10200 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 23.73025 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.71733 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.46050 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 97.43467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 47.46050 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 97.43467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 47.46050 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 97.43467 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TRIMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -Y, X-Y-1, Z-1 REMARK 300 AND -X+Y, -X-1, Z-L. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 13540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 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 82.20400 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 41.10200 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 71.19075 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 A 744 LIES ON A SPECIAL POSITION. 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 48 CD CE NZ REMARK 480 SER A 66 OG REMARK 480 GLU A 86 CG CD OE1 OE2 REMARK 480 ASP A 192 OD1 OD2 REMARK 480 GLU A 221 CG CD OE1 OE2 REMARK 480 GLU A 262 CG CD OE1 OE2 REMARK 480 GLU A 355 OE1 OE2 REMARK 480 GLU A 357 CD OE1 OE2 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 NZ LYS A 219 O HOH A 613 2.18 REMARK 500 CD LYS A 48 O HOH A 745 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 86 CB GLU A 86 CG -0.190 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 LYS A 48 CB - CG - CD ANGL. DEV. = 16.8 DEGREES REMARK 500 GLU A 86 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 LEU A 324 CA - CB - CG ANGL. DEV. = 18.4 DEGREES REMARK 500 LEU A 324 CB - CG - CD2 ANGL. DEV. = -10.6 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 ALA A 168 71.33 -157.54 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 338 ASN A 339 146.47 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 CU A 401 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 126 ND1 REMARK 620 2 CYS A 167 SG 133.9 REMARK 620 3 HIS A 177 ND1 95.7 104.6 REMARK 620 4 MET A 182 SD 88.3 111.8 124.4 REMARK 620 N 1 2 3 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 131 NE2 REMARK 620 2 HIS A 166 NE2 101.3 REMARK 620 3 HIS A 338 NE2 106.0 104.1 REMARK 620 4 NO2 A 501 N 140.4 96.9 103.1 REMARK 620 5 NO2 A 501 O1 171.6 85.1 77.3 32.1 REMARK 620 6 NO2 A 501 O2 109.4 109.6 124.1 31.0 63.0 REMARK 620 7 NO2 A 501 O2 64.5 91.5 46.8 149.9 121.2 158.9 REMARK 620 N 1 2 3 4 5 6 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 NO2 A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZV2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT PH 8.4 REMARK 900 RELATED ID: 2DWT RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT PH 6.0 WITH BOUND NITRITE REMARK 900 RELATED ID: 2DY2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT PH 6.0 DBREF 2DWS A 44 371 UNP Q53239 NIR_RHOSH 44 371 SEQADV 2DWS ASP A 230 UNP Q53239 THR 230 SEE REMARK 999 SEQADV 2DWS ASN A 281 UNP Q53239 LYS 281 SEE REMARK 999 SEQADV 2DWS SER A 319 UNP Q53239 THR 319 SEE REMARK 999 SEQADV 2DWS HIS A 351 UNP Q53239 SER 351 SEE REMARK 999 SEQADV 2DWS VAL A 367 UNP Q53239 TRP 367 SEE REMARK 999 SEQADV 2DWS ALA A 368 UNP Q53239 PRO 368 SEE REMARK 999 SEQRES 1 A 328 LEU PRO ARG VAL LYS HIS THR LEU VAL PRO PRO PRO PHE SEQRES 2 A 328 ALA HIS ALA HIS GLU GLN VAL ALA ALA SER GLY PRO VAL SEQRES 3 A 328 ILE ASN GLU PHE GLU MET ARG ILE ILE GLU LYS GLU VAL SEQRES 4 A 328 GLN LEU ASP GLU ASP ALA TYR LEU GLN ALA MET THR PHE SEQRES 5 A 328 ASP GLY SER ILE PRO GLY PRO LEU MET ILE VAL HIS GLU SEQRES 6 A 328 GLY ASP TYR VAL GLU LEU THR LEU ILE ASN PRO PRO GLU SEQRES 7 A 328 ASN THR MET PRO HIS ASN ILE ASP PHE HIS ALA ALA THR SEQRES 8 A 328 GLY ALA LEU GLY GLY GLY GLY LEU THR LEU ILE ASN PRO SEQRES 9 A 328 GLY GLU LYS VAL VAL LEU ARG PHE LYS ALA THR ARG ALA SEQRES 10 A 328 GLY ALA PHE VAL TYR HIS CYS ALA PRO GLY GLY PRO MET SEQRES 11 A 328 ILE PRO TRP HIS VAL VAL SER GLY MET ALA GLY CYS ILE SEQRES 12 A 328 MET VAL LEU PRO ARG ASP GLY LEU LYS ASP HIS GLU GLY SEQRES 13 A 328 LYS PRO VAL ARG TYR ASP THR VAL TYR TYR ILE GLY GLU SEQRES 14 A 328 SER ASP HIS TYR ILE PRO LYS ASP GLU ASP GLY THR TYR SEQRES 15 A 328 MET ARG PHE SER ASP PRO SER GLU GLY TYR GLU ASP MET SEQRES 16 A 328 VAL ALA VAL MET ASP THR LEU ILE PRO SER HIS ILE VAL SEQRES 17 A 328 PHE ASN GLY ALA VAL GLY ALA LEU THR GLY GLU GLY ALA SEQRES 18 A 328 LEU LYS ALA LYS VAL GLY ASP ASN VAL LEU PHE VAL HIS SEQRES 19 A 328 SER GLN PRO ASN ARG ASP SER ARG PRO HIS LEU ILE GLY SEQRES 20 A 328 GLY HIS GLY ASP LEU VAL TRP GLU THR GLY LYS PHE HIS SEQRES 21 A 328 ASN ALA PRO GLU ARG ASP LEU GLU THR TRP PHE ILE ARG SEQRES 22 A 328 GLY GLY SER ALA GLY ALA ALA LEU TYR LYS PHE LEU GLN SEQRES 23 A 328 PRO GLY VAL TYR ALA TYR VAL ASN HIS ASN LEU ILE GLU SEQRES 24 A 328 ALA VAL HIS LYS GLY ALA THR ALA HIS VAL LEU VAL GLU SEQRES 25 A 328 GLY GLU TRP ASP ASN ASP LEU MET GLU GLN VAL VAL ALA SEQRES 26 A 328 PRO VAL GLY HET CU A 401 1 HET CU A 402 1 HET NO2 A 501 3 HETNAM CU COPPER (II) ION HETNAM NO2 NITRITE ION FORMUL 2 CU 2(CU 2+) FORMUL 4 NO2 N O2 1- FORMUL 5 HOH *249(H2 O) HELIX 1 1 GLY A 135 THR A 143 5 9 HELIX 2 2 PRO A 172 SER A 180 1 9 HELIX 3 3 ASP A 230 THR A 244 1 15 HELIX 4 4 THR A 260 ALA A 264 5 5 HELIX 5 5 ASN A 339 HIS A 345 1 7 SHEET 1 A 3 ARG A 46 LYS A 48 0 SHEET 2 A 3 ILE A 70 ASP A 85 1 O GLU A 72 N VAL A 47 SHEET 3 A 3 ALA A 88 PHE A 95 -1 O LEU A 90 N VAL A 82 SHEET 1 B 4 ARG A 46 LYS A 48 0 SHEET 2 B 4 ILE A 70 ASP A 85 1 O GLU A 72 N VAL A 47 SHEET 3 B 4 TYR A 111 ASN A 118 1 O GLU A 113 N ASN A 71 SHEET 4 B 4 GLU A 149 LYS A 156 -1 O GLU A 149 N ASN A 118 SHEET 1 C 4 LEU A 103 HIS A 107 0 SHEET 2 C 4 ALA A 183 LEU A 189 1 O MET A 187 N MET A 104 SHEET 3 C 4 GLY A 161 HIS A 166 -1 N GLY A 161 O VAL A 188 SHEET 4 C 4 ASP A 129 PHE A 130 -1 N ASP A 129 O HIS A 166 SHEET 1 D 6 HIS A 249 PHE A 252 0 SHEET 2 D 6 THR A 206 HIS A 215 -1 N HIS A 215 O HIS A 249 SHEET 3 D 6 ASN A 272 GLN A 279 1 O VAL A 276 N ILE A 210 SHEET 4 D 6 SER A 319 LYS A 326 -1 O ALA A 323 N PHE A 275 SHEET 5 D 6 GLY A 293 TRP A 297 -1 N TRP A 297 O ALA A 322 SHEET 6 D 6 GLU A 307 LEU A 310 -1 O GLU A 307 N VAL A 296 SHEET 1 E 4 LEU A 265 LYS A 268 0 SHEET 2 E 4 THR A 349 GLU A 355 1 O LEU A 353 N LEU A 265 SHEET 3 E 4 GLY A 331 ASN A 337 -1 N TYR A 335 O ALA A 350 SHEET 4 E 4 PRO A 286 ILE A 289 -1 N ILE A 289 O ALA A 334 LINK ND1 HIS A 126 CU CU A 401 1555 1555 2.11 LINK NE2 HIS A 131 CU CU A 402 1555 1555 2.04 LINK NE2 HIS A 166 CU CU A 402 1555 1555 2.10 LINK SG CYS A 167 CU CU A 401 1555 1555 2.21 LINK ND1 HIS A 177 CU CU A 401 1555 1555 2.05 LINK SD MET A 182 CU CU A 401 1555 1555 2.41 LINK NE2 HIS A 338 CU CU A 402 3665 1555 2.18 LINK CU CU A 402 N NO2 A 501 1555 3665 2.68 LINK CU CU A 402 O1 NO2 A 501 1555 3665 2.50 LINK CU CU A 402 O2 NO2 A 501 1555 3665 1.91 LINK CU CU A 402 O2 NO2 A 501 2655 1555 1.91 CISPEP 1 PRO A 54 PRO A 55 0 8.03 CISPEP 2 ILE A 99 PRO A 100 0 -4.66 SITE 1 AC1 4 HIS A 126 CYS A 167 HIS A 177 MET A 182 SITE 1 AC2 6 ASP A 129 HIS A 131 HIS A 166 HIS A 287 SITE 2 AC2 6 HIS A 338 NO2 A 501 SITE 1 AC3 8 ASP A 129 HIS A 131 HIS A 166 HIS A 287 SITE 2 AC3 8 ILE A 289 HIS A 338 LEU A 340 CU A 402 CRYST1 82.204 82.204 146.152 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 0.012165 0.007023 -0.000001 0.00000 SCALE2 0.000000 0.014046 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.006842 0.00000