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- PDB-1bkj: NADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI -

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Basic information

Entry
Database: PDB / ID: 1bkj
TitleNADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI
ComponentsNADPH-FLAVIN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / LUMINESCENCE / NADP / FLAVOPROTEIN
Function / homology
Function and homology information


FMN reductase (NADPH) / FMN reductase (NADPH) activity / bioluminescence
Similarity search - Function
Flavin oxidoreductase Frp family / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / NADPH-flavin oxidoreductase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsTanner, J.J. / Lei, B. / TU, S.-C. / Krause, K.L.
Citation
Journal: Biochemistry / Year: 1996
Title: Flavin reductase P: structure of a dimeric enzyme that reduces flavin.
Authors: Tanner, J.J. / Lei, B. / Tu, S.C. / Krause, K.L.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Crystallographic Analysis of Nadph:Fmn Oxidoreductase from Vibrio Harveyi
Authors: Tanner, J. / Lei, B. / Liu, M. / TU, S.C. / Krause, K.L.
History
DepositionJul 8, 1998Processing site: BNL
SupersessionJan 13, 1999ID: 1CUM
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: NADPH-FLAVIN OXIDOREDUCTASE
B: NADPH-FLAVIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7706
Polymers52,6672
Non-polymers1,1034
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-88 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.200, 85.900, 58.100
Angle α, β, γ (deg.)90.00, 109.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.351799, -0.317456, -0.880601), (-0.321054, -0.924595, 0.205055), (-0.879296, 0.210583, -0.427193)
Vector: 16.6385, 13.3252, 20.7709)

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Components

#1: Protein NADPH-FLAVIN OXIDOREDUCTASE / FLAVIN REDUCTASE P / FRP / FMN REDUCTASE / NADPH\:FMN OXIDOREDUCTASE


Mass: 26333.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: JM109 / Gene: VIBRIO HARVEYI NADPH\:FMN OXIDOREDUCTASE / Plasmid: PFRP1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q56691, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG60001reservoir
20.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 10, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28 Å / Num. obs: 36163 / % possible obs: 82 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.8→1.9 Å / % possible all: 40.7
Reflection
*PLUS
Num. measured all: 117092
Reflection shell
*PLUS
% possible obs: 40.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→28 Å / Data cutoff low absF: 1.3 / Cross valid method: THROUGHOUT
Details: FMN, PO4 AND WATER PARAMETERS FROM X-PLOR 3.1 DISTRIBUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3540 10 %RANDOM
Rwork0.175 ---
obs0.175 35684 82 %-
Displacement parametersBiso mean: 19.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 72 107 3564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNATOPOLOGY.FMN
X-RAY DIFFRACTION3PARAM.FMN
X-RAY DIFFRACTION4PARAM11.WAT
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_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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