HEADER OXIDOREDUCTASE 20-NOV-11 3VKP TITLE ASSIMILATORY NITRITE REDUCTASE (NII3) - NO2 COMPLEX FROM TOBBACO LEAF TITLE 2 ANALYSED WITH LOW X-RAY DOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 19-587; COMPND 5 SYNONYM: NII3; COMPND 6 EC: 1.7.7.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NICOTIANA TABACUM; SOURCE 3 ORGANISM_COMMON: TOBACCO; SOURCE 4 ORGANISM_TAXID: 4097; SOURCE 5 GENE: NII3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS LOW X-RAY DOSE, 3 ALPHA/BETA DOMAINS, REDUCTASE, SIROHEME, FE4S4, KEYWDS 2 NITRITE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.NAKANO,M.TAKAHASHI,A.SAKAMOTO,H.MORIKAWA,K.KATAYANAGI REVDAT 4 27-DEC-23 3VKP 1 COMPND FORMUL REVDAT 3 08-NOV-23 3VKP 1 REMARK SEQADV LINK REVDAT 2 17-JUL-13 3VKP 1 JRNL REVDAT 1 25-APR-12 3VKP 0 JRNL AUTH S.NAKANO,M.TAKAHASHI,A.SAKAMOTO,H.MORIKAWA,K.KATAYANAGI JRNL TITL THE REDUCTIVE REACTION MECHANISM OF TOBACCO NITRITE JRNL TITL 2 REDUCTASE DERIVED FROM A COMBINATION OF CRYSTAL STRUCTURES JRNL TITL 3 AND ULTRAVIOLET-VISIBLE MICROSPECTROSCOPY JRNL REF PROTEINS V. 80 2035 2012 JRNL REFN ISSN 0887-3585 JRNL PMID 22499059 JRNL DOI 10.1002/PROT.24094 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 134844 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6773 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8903 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 462 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4246 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 922 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : -0.31000 REMARK 3 B33 (A**2) : 0.62000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.714 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4424 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6001 ; 1.217 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 537 ; 5.982 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 205 ;31.399 ;24.195 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 784 ;11.860 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;13.163 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 651 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3327 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2365 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3077 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 762 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.101 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 51 ; 0.144 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 75 ; 0.118 ; 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): 2681 ; 0.455 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4344 ; 0.886 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1754 ; 1.510 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1645 ; 2.471 ; 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 3VKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000095165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : VERTICAL AND HORIZONTAL SILICON REMARK 200 SINGLE CRYSTAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 134915 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : 0.11800 REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.520 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: 3B0G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, TRIS-HCL, MGCL2, MPD, NANO2, REMARK 280 PH 8.5, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 66.55350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 66.55350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 66.55350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 66.55350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 66.55350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.55350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 66.55350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.55350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A1114 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 MET A -28 REMARK 465 GLY A -27 REMARK 465 HIS A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 HIS A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 SER A -16 REMARK 465 SER A -15 REMARK 465 GLY A -14 REMARK 465 HIS A -13 REMARK 465 ILE A -12 REMARK 465 GLU A -11 REMARK 465 GLY A -10 REMARK 465 ARG A -9 REMARK 465 HIS A -8 REMARK 465 MET A -7 REMARK 465 PHE A -6 REMARK 465 SER A -5 REMARK 465 LYS A -4 REMARK 465 ASN A -3 REMARK 465 ALA A -2 REMARK 465 VAL A -1 REMARK 465 LYS A 0 REMARK 465 LEU A 1 REMARK 465 HIS A 2 REMARK 465 ALA A 3 REMARK 465 THR A 4 REMARK 465 PRO A 5 REMARK 465 PRO A 6 REMARK 465 SER A 7 REMARK 465 VAL A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 PRO A 11 REMARK 465 PRO A 12 REMARK 465 THR A 13 REMARK 465 GLY A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 REMARK 465 GLU A 17 REMARK 465 GLU A 556 REMARK 465 ARG A 557 REMARK 465 GLU A 558 REMARK 465 GLU A 559 REMARK 465 THR A 560 REMARK 465 GLU A 561 REMARK 465 ASP A 562 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 O2 NO2 A 606 O HOH A 1054 2.05 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 VAL A 88 -60.19 -128.41 REMARK 500 GLN A 102 63.13 -153.13 REMARK 500 CYS A 137 -177.84 -175.69 REMARK 500 MET A 175 -140.70 52.40 REMARK 500 ASN A 220 63.73 -117.60 REMARK 500 ASN A 304 117.94 -35.23 REMARK 500 VAL A 373 27.52 43.42 REMARK 500 THR A 500 -159.19 -141.95 REMARK 500 ASP A 522 58.96 -90.98 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 LEU A 110 LYS A 111 149.99 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 K A 603 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 371 O REMARK 620 2 GLU A 401 O 148.8 REMARK 620 3 GLN A 402 O 74.2 75.3 REMARK 620 4 ASN A 403 OD1 86.9 91.2 74.6 REMARK 620 5 HOH A1013 O 105.4 77.2 106.2 167.5 REMARK 620 6 HOH A1027 O 133.8 75.7 139.3 78.0 94.5 REMARK 620 7 HOH A1042 O 79.1 128.0 149.7 118.2 67.4 70.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 602 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 440 SG REMARK 620 2 SF4 A 602 S1 107.8 REMARK 620 3 SF4 A 602 S3 114.3 110.3 REMARK 620 4 SF4 A 602 S4 116.4 104.9 102.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 602 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 446 SG REMARK 620 2 SF4 A 602 S1 123.6 REMARK 620 3 SF4 A 602 S2 103.5 103.7 REMARK 620 4 SF4 A 602 S4 112.8 104.1 108.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 602 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 481 SG REMARK 620 2 SF4 A 602 S2 103.0 REMARK 620 3 SF4 A 602 S3 119.3 104.1 REMARK 620 4 SF4 A 602 S4 119.5 107.5 102.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SRM A 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 485 SG REMARK 620 2 SRM A 601 NA 91.0 REMARK 620 3 SRM A 601 NB 92.6 91.3 REMARK 620 4 SRM A 601 NC 88.6 178.9 89.7 REMARK 620 5 SRM A 601 ND 84.7 89.2 177.2 89.8 REMARK 620 6 NO2 A 606 N 177.0 88.8 90.4 91.5 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 602 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 485 SG REMARK 620 2 SF4 A 602 S1 119.9 REMARK 620 3 SF4 A 602 S2 119.1 103.8 REMARK 620 4 SF4 A 602 S3 99.5 108.9 104.2 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 SRM A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO2 A 606 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B0G RELATED DB: PDB REMARK 900 ASSIMILATORY NITRITE REDUCTASE (NII3) FROM TOBBACO LEAF REMARK 900 RELATED ID: 3VKQ RELATED DB: PDB REMARK 900 THE SAME PROTEIN-NO2 COMPLEX WITH MIDDLE X-RAY DOSE REMARK 900 RELATED ID: 3VKR RELATED DB: PDB REMARK 900 THE SAME PROTEIN-NO2 COMPLEX WITH HIGH X-RAY DOSE REMARK 900 RELATED ID: 3VKS RELATED DB: PDB REMARK 900 THE SAME PROTEIN-NO COMPLEX REMARK 900 RELATED ID: 3VKT RELATED DB: PDB REMARK 900 THE SAME PROTEIN-NH2OH COMPLEX DBREF 3VKP A -6 562 UNP Q76KB0 Q76KB0_TOBAC 19 587 SEQADV 3VKP MET A -28 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP GLY A -27 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -26 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -25 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -24 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -23 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -22 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -21 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -20 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -19 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -18 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -17 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP SER A -16 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP SER A -15 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP GLY A -14 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -13 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP ILE A -12 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP GLU A -11 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP GLY A -10 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP ARG A -9 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP HIS A -8 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP MET A -7 UNP Q76KB0 EXPRESSION TAG SEQADV 3VKP ARG A 290 UNP Q76KB0 LYS 315 CONFLICT SEQRES 1 A 591 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 591 SER GLY HIS ILE GLU GLY ARG HIS MET PHE SER LYS ASN SEQRES 3 A 591 ALA VAL LYS LEU HIS ALA THR PRO PRO SER VAL ALA ALA SEQRES 4 A 591 PRO PRO THR GLY ALA PRO GLU VAL ALA ALA GLU ARG LEU SEQRES 5 A 591 GLU PRO ARG VAL GLU GLU LYS ASP GLY TYR TRP ILE LEU SEQRES 6 A 591 LYS GLU GLN PHE ARG LYS GLY ILE ASN PRO GLN GLU LYS SEQRES 7 A 591 VAL LYS ILE GLU LYS GLU PRO MET LYS LEU PHE MET GLU SEQRES 8 A 591 ASN GLY ILE GLU GLU LEU ALA LYS ILE PRO ILE GLU GLU SEQRES 9 A 591 ILE ASP GLN SER LYS LEU THR LYS ASP ASP ILE ASP VAL SEQRES 10 A 591 ARG LEU LYS TRP LEU GLY LEU PHE HIS ARG ARG LYS ASN SEQRES 11 A 591 GLN TYR GLY ARG PHE MET MET ARG LEU LYS LEU PRO ASN SEQRES 12 A 591 GLY VAL THR THR SER ALA GLN THR ARG TYR LEU ALA SER SEQRES 13 A 591 VAL ILE ARG LYS TYR GLY LYS GLU GLY CYS ALA ASP ILE SEQRES 14 A 591 THR THR ARG GLN ASN TRP GLN ILE ARG GLY VAL VAL LEU SEQRES 15 A 591 PRO ASP VAL PRO GLU ILE LEU LYS GLY LEU ALA GLU VAL SEQRES 16 A 591 GLY LEU THR SER LEU GLN SER GLY MET ASP ASN VAL ARG SEQRES 17 A 591 ASN PRO VAL GLY ASN PRO LEU ALA GLY ILE ASP PRO GLU SEQRES 18 A 591 GLU ILE VAL ASP THR ARG PRO TYR THR ASN LEU LEU SER SEQRES 19 A 591 GLN PHE ILE THR GLY ASN SER ARG GLY ASN PRO ALA VAL SEQRES 20 A 591 SER ASN LEU PRO ARG LYS TRP ASN PRO CYS VAL VAL GLY SEQRES 21 A 591 SER HIS ASP LEU TYR GLU HIS PRO HIS ILE ASN ASP LEU SEQRES 22 A 591 ALA TYR MET PRO ALA THR LYS ASP GLY ARG PHE GLY PHE SEQRES 23 A 591 ASN LEU LEU VAL GLY GLY PHE PHE SER ALA LYS ARG CYS SEQRES 24 A 591 ASP GLU ALA ILE PRO LEU ASP ALA TRP VAL PRO ALA ASP SEQRES 25 A 591 ASP VAL VAL PRO VAL CYS ARG ALA ILE LEU GLU ALA PHE SEQRES 26 A 591 ARG ASP LEU GLY PHE ARG GLY ASN ARG GLN LYS CYS ARG SEQRES 27 A 591 MET MET TRP LEU ILE ASP GLU LEU GLY VAL GLU GLY PHE SEQRES 28 A 591 ARG ALA GLU VAL GLU LYS ARG MET PRO GLN GLN GLN LEU SEQRES 29 A 591 GLU ARG ALA SER PRO GLU ASP LEU VAL GLN LYS GLN TRP SEQRES 30 A 591 GLU ARG ARG ASP TYR LEU GLY VAL HIS PRO GLN LYS GLN SEQRES 31 A 591 GLU GLY TYR SER PHE ILE GLY LEU HIS ILE PRO VAL GLY SEQRES 32 A 591 ARG VAL GLN ALA ASP ASP MET ASP GLU LEU ALA ARG LEU SEQRES 33 A 591 ALA ASP GLU TYR GLY SER GLY GLU ILE ARG LEU THR VAL SEQRES 34 A 591 GLU GLN ASN ILE ILE ILE PRO ASN ILE GLU THR SER LYS SEQRES 35 A 591 ILE GLU ALA LEU LEU LYS GLU PRO VAL LEU SER THR PHE SEQRES 36 A 591 SER PRO ASP PRO PRO ILE LEU MET LYS GLY LEU VAL ALA SEQRES 37 A 591 CYS THR GLY ASN GLN PHE CYS GLY GLN ALA ILE ILE GLU SEQRES 38 A 591 THR LYS ALA ARG SER LEU LYS ILE THR GLU GLU VAL GLN SEQRES 39 A 591 ARG GLN VAL SER LEU THR LYS PRO VAL ARG MET HIS TRP SEQRES 40 A 591 THR GLY CYS PRO ASN THR CYS ALA GLN VAL GLN VAL ALA SEQRES 41 A 591 ASP ILE GLY PHE MET GLY CYS LEU THR ARG ASP LYS ASN SEQRES 42 A 591 GLY LYS THR VAL GLU GLY ALA ASP VAL PHE LEU GLY GLY SEQRES 43 A 591 ARG ILE GLY SER ASP SER HIS LEU GLY GLU VAL TYR LYS SEQRES 44 A 591 LYS ALA VAL PRO CYS ASP ASP LEU VAL PRO LEU VAL VAL SEQRES 45 A 591 ASP LEU LEU VAL ASN ASN PHE GLY ALA VAL PRO ARG GLU SEQRES 46 A 591 ARG GLU GLU THR GLU ASP HET SRM A 601 63 HET SF4 A 602 8 HET K A 603 1 HET CL A 604 1 HET CL A 605 1 HET NO2 A 606 3 HETNAM SRM SIROHEME HETNAM SF4 IRON/SULFUR CLUSTER HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION HETNAM NO2 NITRITE ION FORMUL 2 SRM C42 H44 FE N4 O16 FORMUL 3 SF4 FE4 S4 FORMUL 4 K K 1+ FORMUL 5 CL 2(CL 1-) FORMUL 7 NO2 N O2 1- FORMUL 8 HOH *922(H2 O) HELIX 1 1 ALA A 19 GLU A 24 5 6 HELIX 2 2 GLU A 38 ARG A 41 5 4 HELIX 3 3 ASN A 45 LYS A 54 1 10 HELIX 4 4 MET A 57 GLU A 62 1 6 HELIX 5 5 GLY A 64 ALA A 69 1 6 HELIX 6 6 PRO A 72 ASP A 77 1 6 HELIX 7 7 SER A 79 VAL A 88 1 10 HELIX 8 8 ARG A 89 LEU A 93 5 5 HELIX 9 9 LEU A 112 ASN A 114 5 3 HELIX 10 10 SER A 119 LYS A 131 1 13 HELIX 11 11 TYR A 132 GLY A 136 5 5 HELIX 12 12 ASP A 155 VAL A 166 1 12 HELIX 13 13 THR A 197 THR A 209 1 13 HELIX 14 14 ASN A 215 SER A 219 5 5 HELIX 15 15 HIS A 238 ASN A 242 5 5 HELIX 16 16 ASP A 284 GLY A 300 1 17 HELIX 17 17 ASN A 304 CYS A 308 5 5 HELIX 18 18 ARG A 309 GLY A 318 1 10 HELIX 19 19 GLY A 318 MET A 330 1 13 HELIX 20 20 PRO A 331 GLN A 334 5 4 HELIX 21 21 ILE A 371 VAL A 373 5 3 HELIX 22 22 GLN A 377 GLY A 392 1 16 HELIX 23 23 LYS A 413 LEU A 418 1 6 HELIX 24 24 LYS A 419 THR A 425 5 7 HELIX 25 25 PRO A 431 GLY A 436 1 6 HELIX 26 26 THR A 441 PHE A 445 5 5 HELIX 27 27 THR A 453 GLN A 467 1 15 HELIX 28 28 GLN A 487 ALA A 491 5 5 HELIX 29 29 ASP A 537 PHE A 550 1 14 SHEET 1 A 2 VAL A 27 LYS A 30 0 SHEET 2 A 2 TYR A 33 LEU A 36 -1 O TYR A 33 N LYS A 30 SHEET 1 B 5 LEU A 95 HIS A 97 0 SHEET 2 B 5 ARG A 105 ARG A 109 -1 O MET A 107 N PHE A 96 SHEET 3 B 5 TRP A 146 VAL A 152 -1 O ILE A 148 N MET A 108 SHEET 4 B 5 CYS A 137 ILE A 140 -1 N ASP A 139 O GLN A 147 SHEET 5 B 5 ARG A 375 VAL A 376 -1 O VAL A 376 N ALA A 138 SHEET 1 C 5 VAL A 116 THR A 118 0 SHEET 2 C 5 GLU A 395 LEU A 398 -1 O ILE A 396 N THR A 117 SHEET 3 C 5 ILE A 404 GLU A 410 -1 O ILE A 405 N ARG A 397 SHEET 4 C 5 TYR A 364 LEU A 369 -1 N SER A 365 O ILE A 409 SHEET 5 C 5 GLY A 355 PRO A 358 -1 N HIS A 357 O PHE A 366 SHEET 1 D 4 PRO A 227 VAL A 229 0 SHEET 2 D 4 LEU A 244 LYS A 251 1 O LEU A 244 N CYS A 228 SHEET 3 D 4 ARG A 254 VAL A 261 -1 O ASN A 258 N MET A 247 SHEET 4 D 4 ILE A 274 PRO A 281 -1 O ILE A 274 N VAL A 261 SHEET 1 E 2 PHE A 264 PHE A 265 0 SHEET 2 E 2 CYS A 270 ASP A 271 -1 O ASP A 271 N PHE A 264 SHEET 1 F 5 VAL A 438 ALA A 439 0 SHEET 2 F 5 MET A 476 THR A 479 1 O TRP A 478 N VAL A 438 SHEET 3 F 5 ILE A 493 ARG A 501 1 O PHE A 495 N THR A 479 SHEET 4 F 5 THR A 507 LEU A 515 -1 O VAL A 508 N THR A 500 SHEET 5 F 5 GLU A 527 PRO A 534 -1 O TYR A 529 N VAL A 513 SHEET 1 G 2 VAL A 468 SER A 469 0 SHEET 2 G 2 VAL A 553 PRO A 554 -1 O VAL A 553 N SER A 469 LINK O ILE A 371 K K A 603 1555 1555 2.68 LINK O GLU A 401 K K A 603 1555 1555 2.84 LINK O GLN A 402 K K A 603 1555 1555 2.93 LINK OD1 ASN A 403 K K A 603 1555 1555 2.64 LINK SG CYS A 440 FE2 SF4 A 602 1555 1555 2.30 LINK SG CYS A 446 FE3 SF4 A 602 1555 1555 2.26 LINK SG CYS A 481 FE1 SF4 A 602 1555 1555 2.28 LINK SG CYS A 485 FE SRM A 601 1555 1555 2.36 LINK SG CYS A 485 FE4 SF4 A 602 1555 1555 2.30 LINK FE SRM A 601 N NO2 A 606 1555 1555 1.92 LINK K K A 603 O HOH A1013 1555 1555 2.68 LINK K K A 603 O HOH A1027 1555 1555 2.78 LINK K K A 603 O HOH A1042 1555 1555 2.99 SITE 1 AC1 43 PHE A 96 ARG A 98 ARG A 109 THR A 141 SITE 2 AC1 43 THR A 142 ARG A 143 ASN A 145 GLN A 147 SITE 3 AC1 43 ARG A 149 ARG A 223 LYS A 224 ASN A 226 SITE 4 AC1 43 PHE A 264 PHE A 265 SER A 266 ARG A 309 SITE 5 AC1 43 GLN A 402 CYS A 440 THR A 441 CYS A 446 SITE 6 AC1 43 GLN A 448 ASN A 483 THR A 484 CYS A 485 SITE 7 AC1 43 GLN A 487 SF4 A 602 NO2 A 606 HOH A1004 SITE 8 AC1 43 HOH A1005 HOH A1022 HOH A1031 HOH A1039 SITE 9 AC1 43 HOH A1054 HOH A1060 HOH A1065 HOH A1087 SITE 10 AC1 43 HOH A1133 HOH A1166 HOH A1188 HOH A1221 SITE 11 AC1 43 HOH A1285 HOH A1429 HOH A1471 SITE 1 AC2 10 CYS A 440 CYS A 446 ALA A 449 THR A 479 SITE 2 AC2 10 GLY A 480 CYS A 481 ASN A 483 THR A 484 SITE 3 AC2 10 CYS A 485 SRM A 601 SITE 1 AC3 7 ILE A 371 GLU A 401 GLN A 402 ASN A 403 SITE 2 AC3 7 HOH A1013 HOH A1027 HOH A1042 SITE 1 AC4 3 MET A 175 ARG A 179 HOH A1285 SITE 1 AC5 3 ARG A 99 LYS A 100 HOH A1133 SITE 1 AC6 5 ARG A 109 ARG A 179 LYS A 224 SRM A 601 SITE 2 AC6 5 HOH A1054 CRYST1 133.107 133.107 77.796 90.00 90.00 90.00 P 4 21 2 8 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 0.007513 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007513 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012854 0.00000