HEADER OXIDOREDUCTASE 17-AUG-06 2DWT TITLE CU-CONTAINING NITRITE REDUCTASE AT PH 6.0 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 2DWT 1 REMARK LINK REVDAT 6 11-OCT-17 2DWT 1 REMARK REVDAT 5 13-JUL-11 2DWT 1 VERSN REVDAT 4 24-FEB-09 2DWT 1 VERSN REVDAT 3 13-MAR-07 2DWT 1 JRNL REVDAT 2 12-DEC-06 2DWT 1 JRNL REVDAT 1 05-DEC-06 2DWT 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. 1.90 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 24965 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1270 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1812 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2530 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.55000 REMARK 3 B22 (A**2) : -1.55000 REMARK 3 B33 (A**2) : 2.33000 REMARK 3 B12 (A**2) : -0.78000 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): 0.171 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.192 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2571 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3505 ; 1.878 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 7.642 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 111 ;32.707 ;24.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 374 ;14.444 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;18.564 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 379 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2010 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1134 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1697 ; 0.319 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 150 ; 0.155 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.032 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 82 ; 0.199 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.153 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.040 ; 0.200 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): 1696 ; 1.131 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2623 ; 1.622 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1020 ; 2.507 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 882 ; 3.304 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2DWT 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_1000025940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 1.063 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24972 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 24.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36300 REMARK 200 R SYM FOR SHELL (I) : 0.36300 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1ZV2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, MGCL2, NANO2, PEG 4000, PH 6.0, 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 37.37000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.57558 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.04867 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 37.37000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 21.57558 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.04867 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 37.37000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 21.57558 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.04867 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.15116 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 102.09733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 43.15116 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 102.09733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 43.15116 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 102.09733 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: 14440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 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 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 A 532 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 LEU A 44 CD1 CD2 REMARK 480 LYS A 48 CG CD CE NZ REMARK 480 GLU A 74 CD OE1 OE2 REMARK 480 GLU A 86 CD OE1 OE2 REMARK 480 LYS A 200 CG CD CE NZ REMARK 480 ASP A 220 CB CG OD1 OD2 REMARK 480 GLU A 236 OE1 OE2 REMARK 480 GLU A 262 CG CD OE1 OE2 REMARK 480 LYS A 266 CE NZ REMARK 480 LYS A 268 NZ REMARK 480 ARG A 308 NE CZ NH1 NH2 REMARK 480 LYS A 326 NZ REMARK 480 GLU A 357 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 O HOH A 555 O HOH A 603 2.19 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 LYS A 48 CB LYS A 48 CG -0.320 REMARK 500 GLU A 74 CG GLU A 74 CD 0.215 REMARK 500 GLU A 236 CD GLU A 236 OE1 -0.239 REMARK 500 GLU A 236 CD GLU A 236 OE2 -0.323 REMARK 500 GLU A 262 CB GLU A 262 CG -0.284 REMARK 500 LYS A 266 CD LYS A 266 CE 0.410 REMARK 500 LYS A 268 CE LYS A 268 NZ 0.419 REMARK 500 ARG A 308 CD ARG A 308 NE 0.240 REMARK 500 TYR A 333 CE2 TYR A 333 CD2 -0.097 REMARK 500 GLU A 357 CD GLU A 357 OE1 -0.301 REMARK 500 GLU A 357 CD GLU A 357 OE2 -0.280 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 GLU A 74 CB - CG - CD ANGL. DEV. = -19.2 DEGREES REMARK 500 GLU A 74 CG - CD - OE1 ANGL. DEV. = -18.8 DEGREES REMARK 500 GLU A 74 CG - CD - OE2 ANGL. DEV. = 18.4 DEGREES REMARK 500 ASP A 129 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 129 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 220 N - CA - CB ANGL. DEV. = 19.2 DEGREES REMARK 500 GLU A 262 CA - CB - CG ANGL. DEV. = 18.1 DEGREES REMARK 500 ARG A 285 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 285 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 308 CG - CD - NE ANGL. DEV. = -13.4 DEGREES REMARK 500 LYS A 326 CD - CE - NZ ANGL. DEV. = 48.5 DEGREES REMARK 500 GLU A 357 OE1 - CD - OE2 ANGL. DEV. = 15.1 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 91 88.91 -69.74 REMARK 500 ALA A 168 73.65 -161.18 REMARK 500 LEU A 245 12.49 59.35 REMARK 500 ASN A 281 -17.64 -140.50 REMARK 500 PRO A 369 105.86 -49.84 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 131.5 REMARK 620 3 HIS A 177 ND1 98.6 104.0 REMARK 620 4 MET A 182 SD 89.7 108.0 128.0 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 100.3 REMARK 620 3 HIS A 338 NE2 107.4 105.1 REMARK 620 4 NO2 A 501 O1 157.5 98.1 79.9 REMARK 620 5 NO2 A 501 O2 94.0 106.7 137.4 68.2 REMARK 620 6 NO2 A 501 O2 70.8 89.7 43.2 122.2 159.7 REMARK 620 7 NO2 A 501 N 123.8 115.4 103.4 34.7 36.4 144.5 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 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO2 A 502 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: 2DWS RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT PH 8.4 WITH BOUND NITRITE REMARK 900 RELATED ID: 2DY2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT PH 6.0 DBREF 2DWT A 44 372 UNP Q53239 NIR_RHOSH 44 372 SEQADV 2DWT ASP A 230 UNP Q53239 THR 230 SEE REMARK 999 SEQADV 2DWT ASN A 281 UNP Q53239 LYS 281 SEE REMARK 999 SEQADV 2DWT SER A 319 UNP Q53239 THR 319 SEE REMARK 999 SEQADV 2DWT HIS A 351 UNP Q53239 SER 351 SEE REMARK 999 SEQADV 2DWT VAL A 367 UNP Q53239 TRP 367 SEE REMARK 999 SEQADV 2DWT ALA A 368 UNP Q53239 PRO 368 SEE REMARK 999 SEQRES 1 A 329 LEU PRO ARG VAL LYS HIS THR LEU VAL PRO PRO PRO PHE SEQRES 2 A 329 ALA HIS ALA HIS GLU GLN VAL ALA ALA SER GLY PRO VAL SEQRES 3 A 329 ILE ASN GLU PHE GLU MET ARG ILE ILE GLU LYS GLU VAL SEQRES 4 A 329 GLN LEU ASP GLU ASP ALA TYR LEU GLN ALA MET THR PHE SEQRES 5 A 329 ASP GLY SER ILE PRO GLY PRO LEU MET ILE VAL HIS GLU SEQRES 6 A 329 GLY ASP TYR VAL GLU LEU THR LEU ILE ASN PRO PRO GLU SEQRES 7 A 329 ASN THR MET PRO HIS ASN ILE ASP PHE HIS ALA ALA THR SEQRES 8 A 329 GLY ALA LEU GLY GLY GLY GLY LEU THR LEU ILE ASN PRO SEQRES 9 A 329 GLY GLU LYS VAL VAL LEU ARG PHE LYS ALA THR ARG ALA SEQRES 10 A 329 GLY ALA PHE VAL TYR HIS CYS ALA PRO GLY GLY PRO MET SEQRES 11 A 329 ILE PRO TRP HIS VAL VAL SER GLY MET ALA GLY CYS ILE SEQRES 12 A 329 MET VAL LEU PRO ARG ASP GLY LEU LYS ASP HIS GLU GLY SEQRES 13 A 329 LYS PRO VAL ARG TYR ASP THR VAL TYR TYR ILE GLY GLU SEQRES 14 A 329 SER ASP HIS TYR ILE PRO LYS ASP GLU ASP GLY THR TYR SEQRES 15 A 329 MET ARG PHE SER ASP PRO SER GLU GLY TYR GLU ASP MET SEQRES 16 A 329 VAL ALA VAL MET ASP THR LEU ILE PRO SER HIS ILE VAL SEQRES 17 A 329 PHE ASN GLY ALA VAL GLY ALA LEU THR GLY GLU GLY ALA SEQRES 18 A 329 LEU LYS ALA LYS VAL GLY ASP ASN VAL LEU PHE VAL HIS SEQRES 19 A 329 SER GLN PRO ASN ARG ASP SER ARG PRO HIS LEU ILE GLY SEQRES 20 A 329 GLY HIS GLY ASP LEU VAL TRP GLU THR GLY LYS PHE HIS SEQRES 21 A 329 ASN ALA PRO GLU ARG ASP LEU GLU THR TRP PHE ILE ARG SEQRES 22 A 329 GLY GLY SER ALA GLY ALA ALA LEU TYR LYS PHE LEU GLN SEQRES 23 A 329 PRO GLY VAL TYR ALA TYR VAL ASN HIS ASN LEU ILE GLU SEQRES 24 A 329 ALA VAL HIS LYS GLY ALA THR ALA HIS VAL LEU VAL GLU SEQRES 25 A 329 GLY GLU TRP ASP ASN ASP LEU MET GLU GLN VAL VAL ALA SEQRES 26 A 329 PRO VAL GLY LEU HET CU A 401 1 HET CU A 402 1 HET NO2 A 501 3 HET NO2 A 502 3 HETNAM CU COPPER (II) ION HETNAM NO2 NITRITE ION FORMUL 2 CU 2(CU 2+) FORMUL 4 NO2 2(N O2 1-) FORMUL 6 HOH *104(H2 O) HELIX 1 1 GLY A 135 THR A 143 5 9 HELIX 2 2 PRO A 172 VAL A 179 1 8 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 GLY A 101 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 2 LEU A 194 LYS A 195 0 SHEET 2 D 2 PRO A 201 VAL A 202 -1 O VAL A 202 N LEU A 194 SHEET 1 E 6 HIS A 249 PHE A 252 0 SHEET 2 E 6 THR A 206 HIS A 215 -1 N SER A 213 O VAL A 251 SHEET 3 E 6 ASN A 272 GLN A 279 1 O VAL A 276 N ILE A 210 SHEET 4 E 6 SER A 319 LYS A 326 -1 O TYR A 325 N VAL A 273 SHEET 5 E 6 GLY A 293 TRP A 297 -1 N LEU A 295 O LEU A 324 SHEET 6 E 6 GLU A 307 LEU A 310 -1 O GLU A 307 N VAL A 296 SHEET 1 F 4 LEU A 265 LYS A 268 0 SHEET 2 F 4 THR A 349 GLU A 355 1 O LEU A 353 N LEU A 265 SHEET 3 F 4 GLY A 331 ASN A 337 -1 N GLY A 331 O VAL A 354 SHEET 4 F 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 2.32 LINK NE2 HIS A 131 CU CU A 402 1555 1555 2.03 LINK NE2 HIS A 166 CU CU A 402 1555 1555 2.00 LINK SG CYS A 167 CU CU A 401 1555 1555 2.20 LINK ND1 HIS A 177 CU CU A 401 1555 1555 2.09 LINK SD MET A 182 CU CU A 401 1555 1555 2.58 LINK NE2 HIS A 338 CU CU A 402 2555 1555 2.10 LINK CU CU A 402 O1 NO2 A 501 1555 2555 2.46 LINK CU CU A 402 O2 NO2 A 501 1555 2555 1.95 LINK CU CU A 402 O2 NO2 A 501 3555 1555 1.95 LINK CU CU A 402 N NO2 A 501 1555 2555 2.45 CISPEP 1 PRO A 54 PRO A 55 0 5.46 CISPEP 2 ILE A 99 PRO A 100 0 -1.45 SITE 1 AC1 4 HIS A 126 CYS A 167 HIS A 177 MET A 182 SITE 1 AC2 4 HIS A 131 HIS A 166 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 SITE 1 AC4 2 HIS A 60 GLN A 62 CRYST1 74.740 74.740 153.146 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 0.013380 0.007725 0.000000 0.00000 SCALE2 0.000000 0.015450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006530 0.00000