HEADER OXIDOREDUCTASE 10-NOV-12 3ZBM TITLE STRUCTURE OF M92A VARIANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE TITLE 2 FROM RALSTONIA PICKETTII COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.7.2.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA PICKETTII; SOURCE 3 ORGANISM_TAXID: 402626; SOURCE 4 STRAIN: 12J; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-26B; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET26B-RPNIR; SOURCE 11 OTHER_DETAILS: (GENBANK ACCESSION NUMBER. NC_010678 KEYWDS ELECTRON TRANSFER, OXIDOREDUCTASE, PROTON CHANNEL, DENITRIFICATION EXPDTA X-RAY DIFFRACTION AUTHOR S.V.ANTONYUK,C.HAN,R.R.EADY,S.S.HASNAIN REVDAT 4 20-DEC-23 3ZBM 1 REMARK LINK REVDAT 3 23-JAN-19 3ZBM 1 COMPND JRNL HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK ATOM REVDAT 2 17-APR-13 3ZBM 1 JRNL REVDAT 1 03-APR-13 3ZBM 0 JRNL AUTH S.V.ANTONYUK,C.HAN,R.R.EADY,S.S.HASNAIN JRNL TITL STRUCTURES OF PROTEIN-PROTEIN COMPLEXES INVOLVED IN ELECTRON JRNL TITL 2 TRANSFER. JRNL REF NATURE V. 496 123 2013 JRNL REFN ESSN 1476-4687 JRNL PMID 23535590 JRNL DOI 10.1038/NATURE11996 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 40892 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2170 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) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2720 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3427 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 457 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 0.78000 REMARK 3 B12 (A**2) : -0.26000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.334 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3793 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2559 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5218 ; 1.522 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6308 ; 0.888 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 517 ; 6.301 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;38.018 ;24.611 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 615 ;13.237 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.619 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 561 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4356 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 736 ; 0.001 ; 0.020 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): 2361 ; 0.801 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 962 ; 0.242 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3842 ; 1.418 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1432 ; 2.375 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1343 ; 3.654 ; 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. RESIDUES 1-3 AND 460-467 ARE NOT VISIBLE IN THE REMARK 3 ELECTRON DENSITY REMARK 4 REMARK 4 3ZBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1290054780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43074 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 4AWW REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM MES PH 6.5 20% PEG3350, 0.2 REMARK 280 SODIUM CITRATE, 200 MM NACL, PROTEIN CONCENTRATION 7.5 MG/ML 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 64.20500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.06877 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.69667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 64.20500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 37.06877 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.69667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 64.20500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 37.06877 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.69667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.13755 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 57.39333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 74.13755 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 57.39333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 74.13755 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 57.39333 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -209.9 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 A2127 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2135 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2241 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2291 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 4 REMARK 465 ALA A 460 REMARK 465 PRO A 461 REMARK 465 ALA A 462 REMARK 465 LYS A 463 REMARK 465 ALA A 464 REMARK 465 VAL A 465 REMARK 465 ALA A 466 REMARK 465 GLU A 467 REMARK 465 HIS A 468 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 2098 O HOH A 2178 1.65 REMARK 500 O HOH A 2097 O HOH A 2098 1.99 REMARK 500 O HOH A 2131 O HOH A 2258 2.15 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 142 CG - SD - CE ANGL. DEV. = -16.8 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 ARG A 197 75.94 -119.61 REMARK 500 ARG A 197 75.14 -119.37 REMARK 500 GLU A 252 -120.44 45.23 REMARK 500 SER A 290 94.10 -68.80 REMARK 500 GLN A 369 154.65 76.05 REMARK 500 GLN A 369 154.21 76.91 REMARK 500 ASP A 391 87.73 -163.24 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 A2028 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A2097 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A2122 DISTANCE = 6.53 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 CU A1460 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 ND1 REMARK 620 2 CYS A 135 SG 138.9 REMARK 620 3 HIS A 143 ND1 100.6 107.6 REMARK 620 4 MET A 148 SD 84.0 110.7 112.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A1461 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 99 NE2 REMARK 620 2 HIS A 134 NE2 113.9 REMARK 620 3 HIS A 289 NE2 108.1 108.3 REMARK 620 4 HOH A2136 O 103.2 108.9 114.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A1462 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 368 NE2 REMARK 620 2 HEC A1462 NA 93.9 REMARK 620 3 HEC A1462 NB 87.7 90.9 REMARK 620 4 HEC A1462 NC 88.0 177.7 87.9 REMARK 620 5 HEC A1462 ND 91.9 87.7 178.6 93.4 REMARK 620 6 MET A 418 SD 179.0 85.1 92.4 93.0 88.0 REMARK 620 N 1 2 3 4 5 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 1460 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 1461 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1462 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YQB RELATED DB: PDB REMARK 900 STRUCTURE OF P93A VARIANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE REMARK 900 FROM RALSTONIA PICKETTII AT 1.4 A RESOLUTION REMARK 900 RELATED ID: 3ZIY RELATED DB: PDB REMARK 900 STRUCTURE OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA REMARK 900 PICKETTII AT 1.01 A RESOLUTION REMARK 900 RELATED ID: 4AX3 RELATED DB: PDB REMARK 900 STRUCTURE OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA REMARK 900 PICKETTII AT 1.6 A RESOLUTION DBREF 3ZBM A 1 468 UNP E2STD2 E2STD2_9RALS 32 499 SEQADV 3ZBM ALA A 92 UNP E2STD2 MET 123 CONFLICT SEQRES 1 A 468 ALA SER ALA LYS LEU PRO GLY ASP PHE GLY PRO PRO ARG SEQRES 2 A 468 GLY GLU PRO ILE HIS ALA VAL LEU THR SER PRO PRO LEU SEQRES 3 A 468 VAL PRO PRO PRO VAL ASN ARG THR TYR PRO ALA LYS VAL SEQRES 4 A 468 ILE VAL GLU LEU GLU VAL VAL GLU LYS GLU MET GLN ILE SEQRES 5 A 468 SER GLU GLY VAL SER TYR THR PHE TRP THR PHE GLY GLY SEQRES 6 A 468 THR VAL PRO GLY SER PHE ILE ARG VAL ARG GLN GLY ASP SEQRES 7 A 468 THR VAL GLU PHE HIS LEU LYS ASN HIS PRO SER SER LYS SEQRES 8 A 468 ALA PRO HIS ASN ILE ASP LEU HIS GLY VAL THR GLY PRO SEQRES 9 A 468 GLY GLY GLY ALA ALA SER SER PHE THR ALA PRO GLY HIS SEQRES 10 A 468 GLU SER GLN PHE THR PHE LYS ALA LEU ASN GLU GLY ILE SEQRES 11 A 468 TYR VAL TYR HIS CYS ALA THR ALA PRO VAL GLY MET HIS SEQRES 12 A 468 ILE ALA ASN GLY MET TYR GLY LEU ILE LEU VAL GLU PRO SEQRES 13 A 468 PRO GLU GLY LEU PRO LYS VAL ASP HIS GLU TYR TYR VAL SEQRES 14 A 468 MET GLN GLY ASP PHE TYR THR ALA GLY LYS TYR ARG GLU SEQRES 15 A 468 LYS GLY LEU GLN PRO PHE ASP MET GLU LYS ALA ILE ASP SEQRES 16 A 468 GLU ARG PRO SER TYR VAL LEU PHE ASN GLY ALA GLU GLY SEQRES 17 A 468 ALA LEU THR GLY ASP LYS ALA LEU HIS ALA LYS VAL GLY SEQRES 18 A 468 GLU THR VAL ARG ILE PHE VAL GLY ASN GLY GLY PRO ASN SEQRES 19 A 468 LEU VAL SER SER PHE HIS VAL ILE GLY ALA ILE PHE ASP SEQRES 20 A 468 GLN VAL ARG TYR GLU GLY GLY THR ASN VAL GLN LYS ASN SEQRES 21 A 468 VAL GLN THR THR LEU ILE PRO ALA GLY GLY ALA ALA VAL SEQRES 22 A 468 VAL LYS PHE THR ALA ARG VAL PRO GLY SER TYR VAL LEU SEQRES 23 A 468 VAL ASP HIS SER ILE PHE ARG ALA PHE ASN LYS GLY ALA SEQRES 24 A 468 MET ALA ILE LEU LYS ILE ASP GLY ALA GLU ASN LYS LEU SEQRES 25 A 468 VAL TYR SER GLY LYS GLU LEU ASP SER VAL TYR LEU GLY SEQRES 26 A 468 ASP ARG ALA ALA PRO ASN MET SER ALA VAL THR LYS ALA SEQRES 27 A 468 THR GLN ALA SER VAL SER GLY THR LEU THR VAL GLN ASP SEQRES 28 A 468 GLN VAL GLN ALA GLY ARG ALA LEU PHE ALA GLY THR CYS SEQRES 29 A 468 SER VAL CYS HIS GLN GLY ASN GLY ALA GLY LEU PRO GLY SEQRES 30 A 468 VAL PHE PRO PRO LEU ALA LYS SER ASP PHE LEU ALA ALA SEQRES 31 A 468 ASP PRO LYS ARG ALA MET ASN ILE VAL LEU HIS GLY LEU SEQRES 32 A 468 ASN GLY LYS ILE LYS VAL ASN GLY GLN GLU TYR ASP SER SEQRES 33 A 468 VAL MET PRO PRO MET THR GLN LEU ASN ASP ASP GLU VAL SEQRES 34 A 468 ALA ASN ILE LEU THR TYR VAL LEU ASN SER TRP ASP ASN SEQRES 35 A 468 PRO GLY GLY ARG VAL SER ALA GLU ASP VAL LYS LYS VAL SEQRES 36 A 468 ARG ALA GLN PRO ALA PRO ALA LYS ALA VAL ALA GLU HIS HET CU A1460 1 HET CU A1461 1 HET HEC A1462 43 HETNAM CU COPPER (II) ION HETNAM HEC HEME C FORMUL 2 CU 2(CU 2+) FORMUL 4 HEC C34 H34 FE N4 O4 FORMUL 5 HOH *457(H2 O) HELIX 1 1 GLY A 103 ALA A 108 5 6 HELIX 2 2 PRO A 139 ASN A 146 1 8 HELIX 3 3 ASP A 189 ASP A 195 1 7 HELIX 4 4 THR A 211 ALA A 215 5 5 HELIX 5 5 SER A 290 LYS A 297 1 8 HELIX 6 6 ASP A 320 GLY A 325 1 6 HELIX 7 7 ASP A 326 ALA A 328 5 3 HELIX 8 8 MET A 332 SER A 344 1 13 HELIX 9 9 THR A 348 ALA A 361 1 14 HELIX 10 10 CYS A 364 GLN A 369 1 6 HELIX 11 11 SER A 385 ASP A 391 1 7 HELIX 12 12 ASP A 391 GLY A 402 1 12 HELIX 13 13 ASN A 425 ASN A 438 1 14 HELIX 14 14 SER A 448 GLN A 458 1 11 SHEET 1 AA 2 ILE A 17 HIS A 18 0 SHEET 2 AA 2 LYS A 38 SER A 53 -1 O LYS A 38 N ILE A 17 SHEET 1 AB 5 GLU A 118 LYS A 124 0 SHEET 2 AB 5 THR A 79 ASN A 86 -1 O VAL A 80 N PHE A 123 SHEET 3 AB 5 LYS A 38 SER A 53 1 O VAL A 39 N GLU A 81 SHEET 4 AB 5 VAL A 56 PHE A 63 -1 O VAL A 56 N ILE A 52 SHEET 5 AB 5 GLY A 184 GLN A 186 1 O GLY A 184 N SER A 57 SHEET 1 AC 4 GLU A 118 LYS A 124 0 SHEET 2 AC 4 THR A 79 ASN A 86 -1 O VAL A 80 N PHE A 123 SHEET 3 AC 4 LYS A 38 SER A 53 1 O VAL A 39 N GLU A 81 SHEET 4 AC 4 ILE A 17 HIS A 18 -1 O ILE A 17 N ILE A 40 SHEET 1 AD 4 ILE A 72 ARG A 75 0 SHEET 2 AD 4 TYR A 149 GLU A 155 1 O LEU A 151 N ILE A 72 SHEET 3 AD 4 GLY A 129 HIS A 134 -1 O GLY A 129 N VAL A 154 SHEET 4 AD 4 ASP A 97 LEU A 98 -1 O ASP A 97 N HIS A 134 SHEET 1 AE 5 TYR A 200 PHE A 203 0 SHEET 2 AE 5 HIS A 165 PHE A 174 -1 O GLY A 172 N LEU A 202 SHEET 3 AE 5 THR A 223 GLY A 232 1 O THR A 223 N HIS A 165 SHEET 4 AE 5 ALA A 271 THR A 277 -1 O ALA A 272 N VAL A 228 SHEET 5 AE 5 GLN A 248 TYR A 251 -1 O GLN A 248 N LYS A 275 SHEET 1 AF 5 LEU A 216 LYS A 219 0 SHEET 2 AF 5 MET A 300 ASP A 306 1 O ILE A 302 N LEU A 216 SHEET 3 AF 5 GLY A 282 ASP A 288 -1 O GLY A 282 N ILE A 305 SHEET 4 AF 5 SER A 237 ILE A 242 -1 O HIS A 240 N VAL A 287 SHEET 5 AF 5 THR A 263 ILE A 266 -1 O THR A 264 N PHE A 239 SHEET 1 AG 2 LEU A 403 VAL A 409 0 SHEET 2 AG 2 GLN A 412 MET A 418 -1 O GLN A 412 N VAL A 409 LINK SG CYS A 364 CAB HEC A1462 1555 1555 1.82 LINK SG CYS A 367 CAC HEC A1462 1555 1555 2.01 LINK ND1 HIS A 94 CU CU A1460 1555 1555 2.01 LINK NE2 HIS A 99 CU CU A1461 1555 1555 2.03 LINK NE2 HIS A 134 CU CU A1461 1555 1555 2.03 LINK SG CYS A 135 CU CU A1460 1555 1555 2.16 LINK ND1 HIS A 143 CU CU A1460 1555 1555 2.07 LINK SD MET A 148 CU CU A1460 1555 1555 2.61 LINK NE2 HIS A 289 CU CU A1461 2555 1555 2.12 LINK NE2 HIS A 368 FE HEC A1462 1555 1555 2.00 LINK SD MET A 418 FE HEC A1462 1555 1555 2.29 LINK CU CU A1461 O HOH A2136 1555 1555 1.92 CISPEP 1 PRO A 24 PRO A 25 0 4.29 CISPEP 2 VAL A 67 PRO A 68 0 -3.89 CISPEP 3 ALA A 138 PRO A 139 0 -6.95 CISPEP 4 GLY A 232 PRO A 233 0 12.88 SITE 1 AC1 4 HIS A 94 CYS A 135 HIS A 143 MET A 148 SITE 1 AC2 6 HIS A 99 HIS A 134 HIS A 240 HIS A 289 SITE 2 AC2 6 HOH A2136 HOH A2310 SITE 1 AC3 16 THR A 363 CYS A 364 VAL A 366 CYS A 367 SITE 2 AC3 16 HIS A 368 PRO A 380 PRO A 381 LEU A 382 SITE 3 AC3 16 SER A 385 PHE A 387 ASN A 404 GLY A 405 SITE 4 AC3 16 SER A 416 VAL A 417 MET A 418 MET A 421 CRYST1 128.410 128.410 86.090 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 0.007788 0.004496 0.000000 0.00000 SCALE2 0.000000 0.008992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011616 0.00000