HEADER OXIDOREDUCTASE 05-DEC-11 3VLY
TITLE ASSIMILATORY NITRITE REDUCTASE (NII3) - N226K MUTANT - SO3 PARTIAL
TITLE 2 COMPLEX FROM TOBACCO LEAF
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NITRITE REDUCTASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 19-580;
COMPND 5 EC: 1.7.7.1;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: 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 NII3 N226K MUTANT, SO3 PARTIAL COMPLEX, 3 ALPHA/BETA DOMAINS,
KEYWDS 2 REDUCTASE, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.NAKANO,M.TAKAHASHI,A.SAKAMOTO,H.MORIKAWA,K.KATAYANAGI
REVDAT 3 27-DEC-23 3VLY 1 COMPND FORMUL
REVDAT 2 08-NOV-23 3VLY 1 REMARK SEQADV LINK
REVDAT 1 26-SEP-12 3VLY 0
JRNL AUTH S.NAKANO,M.TAKAHASHI,A.SAKAMOTO,H.MORIKAWA,K.KATAYANAGI
JRNL TITL X-RAY CRYSTAL STRUCTURE OF A MUTANT ASSIMILATORY NITRITE
JRNL TITL 2 REDUCTASE THAT SHOWS SULFITE REDUCTASE-LIKE ACTIVITY
JRNL REF CHEM.BIODIVERS. V. 9 1989 2012
JRNL REFN ISSN 1612-1872
JRNL PMID 22976986
JRNL DOI 10.1002/CBDV.201100442
REMARK 2
REMARK 2 RESOLUTION. 1.55 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) : 1.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.99
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 101113
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) : 0.164
REMARK 3 R VALUE (WORKING SET) : 0.164
REMARK 3 FREE R VALUE : 0.176
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 5048
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) : 1.55
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59
REMARK 3 REFLECTION IN BIN (WORKING SET) : 6933
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2200
REMARK 3 BIN FREE R VALUE SET COUNT : 358
REMARK 3 BIN FREE R VALUE : 0.2550
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4248
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 78
REMARK 3 SOLVENT ATOMS : 922
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 22.60
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.61
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.46000
REMARK 3 B22 (A**2) : -0.46000
REMARK 3 B33 (A**2) : 0.91000
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): 0.065
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.001
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4427 ; 0.009 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6003 ; 1.267 ; 1.996
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 537 ; 5.999 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;32.011 ;24.167
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 790 ;12.032 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;12.980 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 651 ; 0.085 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3323 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2293 ; 0.205 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3051 ; 0.304 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 751 ; 0.128 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.233 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 39 ; 0.139 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 71 ; 0.179 ; 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): 2679 ; 0.525 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4344 ; 1.030 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1759 ; 1.837 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1647 ; 3.022 ; 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 3VLY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-11.
REMARK 100 THE DEPOSITION ID IS D_1000095210.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-JUN-10
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 : AR-NE3A
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 : RH COATED COLLIMATING AND
REMARK 200 FOCUSING SI MIRROR
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 : 101449
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550
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 (%) : 99.9
REMARK 200 DATA REDUNDANCY : 14.20
REMARK 200 R MERGE (I) : 0.10700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 13.70
REMARK 200 R MERGE FOR SHELL (I) : 0.45700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.150
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 (%): 53.58
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, TRIS-HCL, MGCL2, MPD, NA2SO3,
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 66.82850
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 66.82850
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 66.82850
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 66.82850
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 66.82850
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.82850
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 66.82850
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.82850
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 375 HOH A1464 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 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 1133 O HOH A 1894 1.77
REMARK 500 OE1 GLU A 383 NH2 ARG A 386 2.05
REMARK 500 O HOH A 1040 O HOH A 1927 2.16
REMARK 500 O HOH A 1191 O HOH A 1344 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 1191 O HOH A 1906 7555 2.13
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 -59.47 -130.70
REMARK 500 GLN A 102 59.96 -151.20
REMARK 500 CYS A 137 -178.38 -176.42
REMARK 500 MET A 175 -139.76 51.76
REMARK 500 ASN A 220 62.02 -117.54
REMARK 500 ASN A 304 117.43 -37.25
REMARK 500 GLN A 332 13.39 57.76
REMARK 500 VAL A 373 28.84 41.91
REMARK 500 ASP A 522 59.72 -93.79
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 150.8
REMARK 620 3 GLN A 402 O 77.2 74.6
REMARK 620 4 ASN A 403 OD1 89.1 90.8 75.0
REMARK 620 5 HOH A1013 O 105.6 75.5 105.8 165.2
REMARK 620 6 HOH A1027 O 131.1 77.4 141.4 79.4 92.0
REMARK 620 7 HOH A1042 O 78.1 126.1 150.8 119.8 66.5 67.7
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 FE4
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 440 SG
REMARK 620 2 SF4 A 602 S1 107.7
REMARK 620 3 SF4 A 602 S2 114.6 110.5
REMARK 620 4 SF4 A 602 S3 116.3 104.6 102.7
REMARK 620 N 1 2 3
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 446 SG
REMARK 620 2 SF4 A 602 S1 123.9
REMARK 620 3 SF4 A 602 S3 112.5 103.7
REMARK 620 4 SF4 A 602 S4 104.0 104.1 107.5
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 118.3
REMARK 620 3 SF4 A 602 S3 119.5 102.5
REMARK 620 4 SF4 A 602 S4 102.9 104.6 107.9
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 91.5
REMARK 620 3 SRM A 601 NB 93.5 90.9
REMARK 620 4 SRM A 601 NC 88.3 179.5 88.7
REMARK 620 5 SRM A 601 ND 84.0 89.2 177.6 91.2
REMARK 620 6 SO3 A 606 S 175.3 93.0 87.9 87.2 94.5
REMARK 620 N 1 2 3 4 5
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 485 SG
REMARK 620 2 SF4 A 602 S1 118.2
REMARK 620 3 SF4 A 602 S2 100.0 109.0
REMARK 620 4 SF4 A 602 S4 119.8 103.7 105.0
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 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 SO3 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: 3VLX RELATED DB: PDB
REMARK 900 RELATED ID: 3VLZ RELATED DB: PDB
REMARK 900 RELATED ID: 3VM0 RELATED DB: PDB
REMARK 900 RELATED ID: 3VM1 RELATED DB: PDB
DBREF 3VLY A -6 555 UNP Q76KB0 Q76KB0_TOBAC 19 580
SEQADV 3VLY MET A -28 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY GLY A -27 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -26 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -25 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -24 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -23 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -22 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -21 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -20 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -19 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -18 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -17 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY SER A -16 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY SER A -15 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY GLY A -14 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -13 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY ILE A -12 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY GLU A -11 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY GLY A -10 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY ARG A -9 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY HIS A -8 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY MET A -7 UNP Q76KB0 EXPRESSION TAG
SEQADV 3VLY LYS A 226 UNP Q76KB0 ASN 251 ENGINEERED MUTATION
SEQADV 3VLY ARG A 290 UNP Q76KB0 LYS 315 CONFLICT
SEQRES 1 A 584 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER
SEQRES 2 A 584 SER GLY HIS ILE GLU GLY ARG HIS MET PHE SER LYS ASN
SEQRES 3 A 584 ALA VAL LYS LEU HIS ALA THR PRO PRO SER VAL ALA ALA
SEQRES 4 A 584 PRO PRO THR GLY ALA PRO GLU VAL ALA ALA GLU ARG LEU
SEQRES 5 A 584 GLU PRO ARG VAL GLU GLU LYS ASP GLY TYR TRP ILE LEU
SEQRES 6 A 584 LYS GLU GLN PHE ARG LYS GLY ILE ASN PRO GLN GLU LYS
SEQRES 7 A 584 VAL LYS ILE GLU LYS GLU PRO MET LYS LEU PHE MET GLU
SEQRES 8 A 584 ASN GLY ILE GLU GLU LEU ALA LYS ILE PRO ILE GLU GLU
SEQRES 9 A 584 ILE ASP GLN SER LYS LEU THR LYS ASP ASP ILE ASP VAL
SEQRES 10 A 584 ARG LEU LYS TRP LEU GLY LEU PHE HIS ARG ARG LYS ASN
SEQRES 11 A 584 GLN TYR GLY ARG PHE MET MET ARG LEU LYS LEU PRO ASN
SEQRES 12 A 584 GLY VAL THR THR SER ALA GLN THR ARG TYR LEU ALA SER
SEQRES 13 A 584 VAL ILE ARG LYS TYR GLY LYS GLU GLY CYS ALA ASP ILE
SEQRES 14 A 584 THR THR ARG GLN ASN TRP GLN ILE ARG GLY VAL VAL LEU
SEQRES 15 A 584 PRO ASP VAL PRO GLU ILE LEU LYS GLY LEU ALA GLU VAL
SEQRES 16 A 584 GLY LEU THR SER LEU GLN SER GLY MET ASP ASN VAL ARG
SEQRES 17 A 584 ASN PRO VAL GLY ASN PRO LEU ALA GLY ILE ASP PRO GLU
SEQRES 18 A 584 GLU ILE VAL ASP THR ARG PRO TYR THR ASN LEU LEU SER
SEQRES 19 A 584 GLN PHE ILE THR GLY ASN SER ARG GLY ASN PRO ALA VAL
SEQRES 20 A 584 SER ASN LEU PRO ARG LYS TRP LYS PRO CYS VAL VAL GLY
SEQRES 21 A 584 SER HIS ASP LEU TYR GLU HIS PRO HIS ILE ASN ASP LEU
SEQRES 22 A 584 ALA TYR MET PRO ALA THR LYS ASP GLY ARG PHE GLY PHE
SEQRES 23 A 584 ASN LEU LEU VAL GLY GLY PHE PHE SER ALA LYS ARG CYS
SEQRES 24 A 584 ASP GLU ALA ILE PRO LEU ASP ALA TRP VAL PRO ALA ASP
SEQRES 25 A 584 ASP VAL VAL PRO VAL CYS ARG ALA ILE LEU GLU ALA PHE
SEQRES 26 A 584 ARG ASP LEU GLY PHE ARG GLY ASN ARG GLN LYS CYS ARG
SEQRES 27 A 584 MET MET TRP LEU ILE ASP GLU LEU GLY VAL GLU GLY PHE
SEQRES 28 A 584 ARG ALA GLU VAL GLU LYS ARG MET PRO GLN GLN GLN LEU
SEQRES 29 A 584 GLU ARG ALA SER PRO GLU ASP LEU VAL GLN LYS GLN TRP
SEQRES 30 A 584 GLU ARG ARG ASP TYR LEU GLY VAL HIS PRO GLN LYS GLN
SEQRES 31 A 584 GLU GLY TYR SER PHE ILE GLY LEU HIS ILE PRO VAL GLY
SEQRES 32 A 584 ARG VAL GLN ALA ASP ASP MET ASP GLU LEU ALA ARG LEU
SEQRES 33 A 584 ALA ASP GLU TYR GLY SER GLY GLU ILE ARG LEU THR VAL
SEQRES 34 A 584 GLU GLN ASN ILE ILE ILE PRO ASN ILE GLU THR SER LYS
SEQRES 35 A 584 ILE GLU ALA LEU LEU LYS GLU PRO VAL LEU SER THR PHE
SEQRES 36 A 584 SER PRO ASP PRO PRO ILE LEU MET LYS GLY LEU VAL ALA
SEQRES 37 A 584 CYS THR GLY ASN GLN PHE CYS GLY GLN ALA ILE ILE GLU
SEQRES 38 A 584 THR LYS ALA ARG SER LEU LYS ILE THR GLU GLU VAL GLN
SEQRES 39 A 584 ARG GLN VAL SER LEU THR LYS PRO VAL ARG MET HIS TRP
SEQRES 40 A 584 THR GLY CYS PRO ASN THR CYS ALA GLN VAL GLN VAL ALA
SEQRES 41 A 584 ASP ILE GLY PHE MET GLY CYS LEU THR ARG ASP LYS ASN
SEQRES 42 A 584 GLY LYS THR VAL GLU GLY ALA ASP VAL PHE LEU GLY GLY
SEQRES 43 A 584 ARG ILE GLY SER ASP SER HIS LEU GLY GLU VAL TYR LYS
SEQRES 44 A 584 LYS ALA VAL PRO CYS ASP ASP LEU VAL PRO LEU VAL VAL
SEQRES 45 A 584 ASP LEU LEU VAL ASN ASN PHE GLY ALA VAL PRO ARG
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 SO3 A 606 4
HETNAM SRM SIROHEME
HETNAM SF4 IRON/SULFUR CLUSTER
HETNAM K POTASSIUM ION
HETNAM CL CHLORIDE ION
HETNAM SO3 SULFITE 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 SO3 O3 S 2-
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 TYR A 132 1 14
HELIX 11 11 GLY A 133 GLY A 136 5 4
HELIX 12 12 ASP A 155 VAL A 166 1 12
HELIX 13 13 THR A 197 GLY A 210 1 14
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 ARG A 329 1 21
HELIX 19 19 MET A 330 GLN A 334 5 5
HELIX 20 20 ILE A 371 VAL A 373 5 3
HELIX 21 21 GLN A 377 GLY A 392 1 16
HELIX 22 22 LYS A 413 LYS A 419 1 7
HELIX 23 23 GLU A 420 THR A 425 5 6
HELIX 24 24 PRO A 431 GLY A 436 1 6
HELIX 25 25 THR A 441 PHE A 445 5 5
HELIX 26 26 THR A 453 GLN A 467 1 15
HELIX 27 27 GLN A 487 ALA A 491 5 5
HELIX 28 28 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 5 VAL A 438 ALA A 439 0
SHEET 2 E 5 MET A 476 THR A 479 1 O TRP A 478 N VAL A 438
SHEET 3 E 5 ILE A 493 ARG A 501 1 O PHE A 495 N THR A 479
SHEET 4 E 5 THR A 507 LEU A 515 -1 O VAL A 508 N THR A 500
SHEET 5 E 5 GLU A 527 PRO A 534 -1 O TYR A 529 N VAL A 513
SHEET 1 F 2 VAL A 468 SER A 469 0
SHEET 2 F 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 2.58
LINK O GLU A 401 K K A 603 1555 1555 2.86
LINK O GLN A 402 K K A 603 1555 1555 2.85
LINK OD1 ASN A 403 K K A 603 1555 1555 2.57
LINK SG CYS A 440 FE4 SF4 A 602 1555 1555 2.30
LINK SG CYS A 446 FE2 SF4 A 602 1555 1555 2.29
LINK SG CYS A 481 FE1 SF4 A 602 1555 1555 2.28
LINK SG CYS A 485 FE SRM A 601 1555 1555 2.39
LINK SG CYS A 485 FE3 SF4 A 602 1555 1555 2.30
LINK FE SRM A 601 S SO3 A 606 1555 1555 2.29
LINK K K A 603 O HOH A1013 1555 1555 2.46
LINK K K A 603 O HOH A1027 1555 1555 2.67
LINK K K A 603 O HOH A1042 1555 1555 3.17
SITE 1 AC1 45 PHE A 96 ARG A 98 ARG A 109 THR A 141
SITE 2 AC1 45 THR A 142 ARG A 143 ASN A 145 GLN A 147
SITE 3 AC1 45 ARG A 149 ARG A 223 LYS A 224 LYS A 226
SITE 4 AC1 45 PHE A 264 PHE A 265 SER A 266 ARG A 309
SITE 5 AC1 45 GLN A 402 CYS A 440 THR A 441 CYS A 446
SITE 6 AC1 45 GLN A 448 ASN A 483 THR A 484 CYS A 485
SITE 7 AC1 45 GLN A 487 SF4 A 602 SO3 A 606 HOH A1004
SITE 8 AC1 45 HOH A1005 HOH A1022 HOH A1039 HOH A1040
SITE 9 AC1 45 HOH A1054 HOH A1060 HOH A1065 HOH A1087
SITE 10 AC1 45 HOH A1133 HOH A1166 HOH A1188 HOH A1221
SITE 11 AC1 45 HOH A1285 HOH A1429 HOH A1471 HOH A1894
SITE 12 AC1 45 HOH A1927
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 6 ILE A 371 GLU A 401 GLN A 402 ASN A 403
SITE 2 AC3 6 HOH A1013 HOH A1027
SITE 1 AC4 5 PHE A 96 MET A 175 ARG A 179 HOH A1054
SITE 2 AC4 5 HOH A1285
SITE 1 AC5 3 ARG A 99 LYS A 100 HOH A1133
SITE 1 AC6 7 ARG A 109 ARG A 179 LYS A 224 LYS A 226
SITE 2 AC6 7 SRM A 601 HOH A1022 HOH A1054
CRYST1 133.657 133.657 77.823 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 0.007482 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007482 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012850 0.00000
(ATOM LINES ARE NOT SHOWN.)
END