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- PDB-5gv8: Structure of NADH-cytochrome b5 reductase refined with the multip... -

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Basic information

Entry
Database: PDB / ID: 5gv8
TitleStructure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.78A
ComponentsNADH-cytochrome b5 reductase 3
KeywordsOXIDOREDUCTASE / electron transfer / flavoprotein
Function / homology
Function and homology information


cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / cholesterol biosynthetic process / FAD binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / endoplasmic reticulum membrane / mitochondrion
Similarity search - Function
NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type ...NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADH-cytochrome b5 reductase 3
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.78 Å
AuthorsTakaba, K. / Takeda, K. / Miki, K.
CitationJournal: Sci Rep / Year: 2017
Title: Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase.
Authors: Takaba, K. / Takeda, K. / Kosugi, M. / Tamada, T. / Miki, K.
History
DepositionSep 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Data collection / Refinement description / Category: diffrn_source / pdbx_refine / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0286
Polymers30,8741
Non-polymers1,1545
Water10,953608
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.480, 72.108, 84.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADH-cytochrome b5 reductase 3 / Cytochrome b5 reductase / Diaphorase-1


Mass: 30873.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P83686, cytochrome-b5 reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 4000, DTT, K-phos buffer

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Data collection

DiffractionMean temperature: 40 K
Ambient temp details: The author used a cryo-stream of helium.
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.65 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 0.78→31.9 Å / Num. obs: 332946 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rsym value: 0.071 / Net I/σ(I): 28.8
Reflection shellResolution: 0.78→0.79 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.1 / % possible all: 89.5

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Processing

Software
NameVersionClassification
SHELXLrefinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NDH

1ndh


Resolution: 0.78→31.9 Å / Cross valid method: FREE R-VALUE
Details: The model was finally refined with aspherical atomic model by using MOPRO program.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 --RANDOM SELECTION
Rwork0.122 ---
obs-332946 99.1 %-
Refinement stepCycle: LAST / Resolution: 0.78→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 77 608 2845

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