HEADER OXIDOREDUCTASE 27-JUN-05 2A3T TITLE CU-CONTAINING NITRITE REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 44-371; COMPND 5 SYNONYM: CU-NIR; COMPND 6 EC: 1.7.2.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER SPHAEROIDES; SOURCE 3 ORGANISM_TAXID: 1063; SOURCE 4 GENE: NIRK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS COPPER PROTEIN, NITRITE REDUCTION, DENITRIFICATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.JACOBSON,H.GUO,K.OLESEN,M.OKVIST,R.NEUTZE,L.SJOLIN REVDAT 6 23-AUG-23 2A3T 1 REMARK LINK REVDAT 5 07-MAR-18 2A3T 1 REMARK REVDAT 4 13-JUL-11 2A3T 1 VERSN REVDAT 3 24-FEB-09 2A3T 1 VERSN REVDAT 2 23-AUG-05 2A3T 1 JRNL REVDAT 1 02-AUG-05 2A3T 0 JRNL AUTH F.JACOBSON,H.GUO,K.OLESEN,M.OKVIST,R.NEUTZE,L.SJOLIN JRNL TITL STRUCTURES OF THE OXIDIZED AND REDUCED FORMS OF NITRITE JRNL TITL 2 REDUCTASE FROM RHODOBACTER SPHAEROIDES 2.4.3 AT HIGH PH: JRNL TITL 3 CHANGES IN THE INTERACTIONS OF THE TYPE 2 COPPER. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1190 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 16131751 JRNL DOI 10.1107/S0907444905017488 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23444 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1257 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1712 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.1800 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.2090 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 : 236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.65000 REMARK 3 B22 (A**2) : -0.65000 REMARK 3 B33 (A**2) : 0.97000 REMARK 3 B12 (A**2) : -0.32000 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): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2599 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3541 ; 1.461 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 327 ; 6.844 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;35.361 ;24.237 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 395 ;13.215 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.223 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 379 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2035 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1113 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1726 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 233 ; 0.123 ; 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): 95 ; 0.168 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.129 ; 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): 1680 ; 0.932 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2623 ; 1.353 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1051 ; 2.219 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 918 ; 3.465 ; 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 : 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: NULL REMARK 4 REMARK 4 2A3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033452. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-02 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) : 1.017 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24723 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 36.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07900 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) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 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: 1ZV2 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): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MGCL2, TRIS, PH 8.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 36.21800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.91047 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.36300 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 36.21800 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 20.91047 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.36300 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 36.21800 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 20.91047 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.36300 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.82094 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 98.72600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 41.82094 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 98.72600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 41.82094 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 98.72600 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 UNIT IS A TRIMER AND CAN BE GENERATED FROM REMARK 300 THE MONOMER IN THE ASYMMETRIC UNIT BY APPLYING THE SYMMETRY REMARK 300 OPERATIONS: -Y, X-Y, Z AND -X+Y, -X, Z 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: 13690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -126.0 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 72.43600 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 36.21800 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 62.73142 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 672 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 MET A 124 CE REMARK 480 GLU A 236 CD OE1 OE2 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 236 CG GLU A 236 CD 0.117 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 MET A 124 CG - SD - CE ANGL. DEV. = 10.3 DEGREES REMARK 500 VAL A 207 CB - CA - C ANGL. DEV. = -12.2 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 68.98 -153.22 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 339 149.63 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 131.4 REMARK 620 3 HIS A 177 ND1 97.0 112.0 REMARK 620 4 MET A 182 SD 86.6 110.8 117.6 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 107.5 REMARK 620 3 HIS A 338 NE2 106.0 110.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD1 REMARK 620 2 THR A 224 OG1 95.3 REMARK 620 3 HOH A 557 O 88.5 97.3 REMARK 620 4 HOH A 558 O 176.5 87.6 89.1 REMARK 620 5 HOH A 559 O 88.6 80.4 176.1 93.8 REMARK 620 6 HOH A 568 O 87.5 173.2 89.0 89.9 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 585 O REMARK 620 2 HOH A 589 O 91.0 REMARK 620 3 HOH A 725 O 95.2 87.6 REMARK 620 4 HOH A 726 O 85.8 87.4 174.9 REMARK 620 5 HOH A 728 O 93.6 173.5 87.4 97.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 562 O REMARK 620 2 HOH A 705 O 78.7 REMARK 620 3 HOH A 727 O 88.1 93.9 REMARK 620 4 HOH A 732 O 88.1 98.5 166.0 REMARK 620 N 1 2 3 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 MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZV2 RELATED DB: PDB REMARK 900 OXIDISED NITRITE REDUCTASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHOR STATES THAT RESIDUES ASP 230, ASN 281, SER 319, REMARK 999 HIS 351, VAL 367, ALA 368 ARE CORRECT BASED ON THE ELECTRON REMARK 999 DENSITY. DBREF 2A3T A 44 371 UNP Q53239 NIR_RHOSH 44 371 SEQADV 2A3T ASP A 230 UNP Q53239 THR 230 SEE REMARK 999 SEQADV 2A3T ASN A 281 UNP Q53239 LYS 281 SEE REMARK 999 SEQADV 2A3T SER A 319 UNP Q53239 THR 319 SEE REMARK 999 SEQADV 2A3T HIS A 351 UNP Q53239 SER 351 SEE REMARK 999 SEQADV 2A3T VAL A 367 UNP Q53239 TRP 367 SEE REMARK 999 SEQADV 2A3T 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 MG A 501 1 HET MG A 502 1 HET MG A 503 1 HETNAM CU COPPER (II) ION HETNAM MG MAGNESIUM ION FORMUL 2 CU 2(CU 2+) FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *236(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 PHE A 155 N VAL A 112 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 HIS A 351 N LEU A 265 SHEET 3 E 4 GLY A 331 ASN A 337 -1 N GLY A 331 O VAL A 354 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 2.19 LINK NE2 HIS A 131 CU CU A 402 1555 1555 2.04 LINK NE2 HIS A 166 CU CU A 402 1555 1555 2.07 LINK SG CYS A 167 CU CU A 401 1555 1555 2.23 LINK ND1 HIS A 177 CU CU A 401 1555 1555 2.11 LINK SD MET A 182 CU CU A 401 1555 1555 2.45 LINK OD1 ASP A 220 MG MG A 501 1555 1555 2.06 LINK OG1 THR A 224 MG MG A 501 1555 1555 2.19 LINK NE2 HIS A 338 CU CU A 402 2655 1555 2.11 LINK MG MG A 501 O HOH A 557 1555 1555 2.05 LINK MG MG A 501 O HOH A 558 1555 9664 2.06 LINK MG MG A 501 O HOH A 559 1555 1555 2.08 LINK MG MG A 501 O HOH A 568 1555 9664 2.03 LINK MG MG A 502 O HOH A 585 1555 9664 2.17 LINK MG MG A 502 O HOH A 589 1555 9664 2.38 LINK MG MG A 502 O HOH A 725 1555 9664 2.05 LINK MG MG A 502 O HOH A 726 1555 1555 2.13 LINK MG MG A 502 O HOH A 728 1555 1555 2.08 LINK MG MG A 503 O HOH A 562 1555 1555 2.31 LINK MG MG A 503 O HOH A 705 1555 1555 2.26 LINK MG MG A 503 O HOH A 727 1555 1555 2.02 LINK MG MG A 503 O HOH A 732 1555 1555 2.03 CISPEP 1 PRO A 54 PRO A 55 0 5.06 CISPEP 2 ILE A 99 PRO A 100 0 2.25 SITE 1 AC1 4 HIS A 126 CYS A 167 HIS A 177 MET A 182 SITE 1 AC2 4 ASP A 129 HIS A 131 HIS A 166 HIS A 338 SITE 1 AC3 6 ASP A 220 THR A 224 HOH A 557 HOH A 558 SITE 2 AC3 6 HOH A 559 HOH A 568 SITE 1 AC4 5 HOH A 585 HOH A 589 HOH A 725 HOH A 726 SITE 2 AC4 5 HOH A 728 SITE 1 AC5 4 HOH A 562 HOH A 705 HOH A 727 HOH A 732 CRYST1 72.436 72.436 148.089 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 0.013805 0.007970 0.000000 0.00000 SCALE2 0.000000 0.015941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006753 0.00000