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- PDB-2bkj: NADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI COMPLEXED WITH NAD+ -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2bkj
TitleNADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI COMPLEXED WITH NAD+
ComponentsFLAVIN REDUCTASE
KeywordsOXIDOREDUCTASE / FRP
Function / homology
Function and homology information


FMN reductase (NADPH) / FMN reductase (NAD(P)H) activity / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADPH-flavin oxidoreductase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsTanner, J.J. / TU, S.-C. / Krause, K.L.
Citation
Journal: Protein Sci. / Year: 1999
Title: Unusual folded conformation of nicotinamide adenine dinucleotide bound to flavin reductase P.
Authors: Tanner, J.J. / Tu, S.C. / Barbour, L.J. / Barnes, C.L. / Krause, K.L.
#1: 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.
#2: 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 23, 1998Processing site: BNL
Revision 1.0Sep 10, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FLAVIN REDUCTASE
B: FLAVIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2435
Polymers52,6672
Non-polymers1,5763
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-79 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.200, 85.900, 59.200
Angle α, β, γ (deg.)90.00, 114.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.351634, -0.373835, -0.858255), (-0.377181, -0.895672, 0.235599), (-0.85679, 0.240873, -0.455952)
Vector: 17.1469, 12.5814, 21.5066)

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Components

#1: Protein FLAVIN REDUCTASE / / 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 / 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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / Details: Tanner, J., (1994) J.Mol.Biol., 241, 283.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-8 mg/mlenzyme1drop
210 mMTris-HCl1drop
330 %PEG60001reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / 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: 2.08→32 Å / Num. obs: 23598 / % possible obs: 84 % / Redundancy: 2.1 % / Rsym value: 0.034
Reflection shellResolution: 2.08→2.2 Å / % possible all: 38
Reflection
*PLUS
Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 38 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
MADNESdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BKJ

1bkj


Resolution: 2.08→32 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: PARAMETERS AND TOPOLOGY FILES FROM X-PLOR 3.851 DISTRIBUTION. FREE R VALUE TEST SET SELECTION IS THE SAME TEST SET THAT USED IN DETERMINATION OF PDB ENTRY 1BKJ.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2159 10 %RANDOM
Rwork0.185 ---
obs0.185 23598 84 %-
Refinement stepCycle: LAST / Resolution: 2.08→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 106 73 3575
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.08→2.24 Å
RfactorNum. reflection% reflection
Rfree0.259 219 10 %
Rwork0.224 2466 -
obs--48 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNATOPOLOGY.FMN
X-RAY DIFFRACTION3PARAM.FMN,PARAM.NADTOPOLOGY.NAD
X-RAY DIFFRACTION4PARAM11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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