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- PDB-1vfr: THE MAJOR NAD(P)H:FMN OXIDOREDUCTASE FROM VIBRIO FISCHERI -

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Basic information

Entry
Database: PDB / ID: 1vfr
TitleTHE MAJOR NAD(P)H:FMN OXIDOREDUCTASE FROM VIBRIO FISCHERI
ComponentsNAD(P)H\:FMN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / NAD(P)H / FMN / VIBRIO FISCHERI / BIOLUMINESCENCE
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / bioluminescence / oxidoreductase activity
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Major NAD(P)H-flavin oxidoreductase
Similarity search - Component
Biological speciesAliivibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsKoike, H. / Sasaki, H. / Kobori, T. / Zenno, S. / Saigo, K. / Murphy, M.E.P. / Adman, E.T. / Tanokura, M.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: 1.8 A crystal structure of the major NAD(P)H:FMN oxidoreductase of a bioluminescent bacterium, Vibrio fischeri: overall structure, cofactor and substrate-analog binding, and comparison with related flavoproteins.
Authors: Koike, H. / Sasaki, H. / Kobori, T. / Zenno, S. / Saigo, K. / Murphy, M.E. / Adman, E.T. / Tanokura, M.
#1: Journal: J.Struct.Biol. / Year: 1996
Title: Crystallization and Preliminary Crystallographic Analysis of the Major Nad(P)H: Fmn Oxidoreductase of Vibrio Fischeri Atcc 7744
Authors: Koike, H. / Sasaki, H. / Tanokura, M. / Zenno, S. / Saigo, K.
History
DepositionJan 9, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)H\:FMN OXIDOREDUCTASE
B: NAD(P)H\:FMN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4254
Polymers49,5122
Non-polymers9132
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-40 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.600, 63.300, 74.400
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.408754, 0.030328, 0.912141), (-0.017024, -0.999527, 0.025604), (0.912486, -0.005062, 0.409077)
Vector: 71.27158, 31.34125, -46.42405)

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Components

#1: Protein NAD(P)H\:FMN OXIDOREDUCTASE / FRASE I / FMN REDUCTASE


Mass: 24755.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio fischeri (bacteria) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 105
References: UniProt: P46072, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 48 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
230 %(w/v)PEG40001reservoir
30.2 Msodium acetate1reservoir
40.1 mMFMN1reservoir
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 40445 / % possible obs: 91.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.79→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.6 / % possible all: 74.4
Reflection
*PLUS
Num. obs: 39895 / Num. measured all: 180543

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2319 4.9 %SHELLS
Rwork0.187 ---
obs0.187 43159 91.3 %-
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 62 183 3713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.83
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.33
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.31 285 5.3 %
Rwork0.27 3819 -
obs--76.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.83
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33
LS refinement shell
*PLUS
Rfactor obs: 0.27

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