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- PDB-9v69: X-ray crystal structure of the two-electron reduced form of wild ... -

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Basic information

Entry
Database: PDB / ID: 9v69
TitleX-ray crystal structure of the two-electron reduced form of wild type b5R
ComponentsNADH-cytochrome b5 reductase 3
KeywordsOXIDOREDUCTASE / fatty acid synthesis / methemoglobin reduction / xenobiotic oxidation / antioxidant defense
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 / 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
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH-cytochrome b5 reductase 3
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsHirano, Y. / Kurihara, K. / Kusaka, K. / Ostermann, A. / Hikita, M. / Kimura, S. / Miki, K. / Tamada, T.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR17G7 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)Photon and Quantum Basic Research Coordinated Development Program Japan
Japan Society for the Promotion of Science (JSPS)JP20K06523 Japan
Japan Society for the Promotion of Science (JSPS)JP17K07325 Japan
Japan Society for the Promotion of Science (JSPS)JP2544037 Japan
CitationJournal: Structure / Year: 2025
Title: Structural basis of hydride and proton transfer reactions revealed by the detection of hydrogen atoms in mammalian NADH-cytochrome b 5 reductase.
Authors: Hirano, Y. / Kurihara, K. / Kusaka, K. / Ostermann, A. / Hikita, M. / Kimura, S. / Miki, K. / Tamada, T.
History
DepositionMay 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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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)32,3243
Polymers30,8731
Non-polymers1,4512
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-14 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.021, 79.255, 86.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein NADH-cytochrome b5 reductase 3 / B5R / Cytochrome b5 reductase / Diaphorase-1


Mass: 30872.689 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-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN
Nonpolymer detailsThe flavin cofactor in this structure is the hydroquinone form (FADH-), formula C27 H34 N9 O15 P2

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7
Details: 30% PEG 3350, 10mM potassium phosphate, 1mM dithiothreitol, 0.1mM NADH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.96→50 Å / Num. obs: 191725 / % possible obs: 95.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23
Reflection shellResolution: 0.96→0.98 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 7020 / CC1/2: 0.818

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Processing

Software
NameClassification
SHELXLrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.96→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1481 9693 5.06 %Select the same reflections as PDB code 3W2G
Rwork0.1265 181968 --
obs-181968 93.4 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 97 450 2718
LS refinement shellResolution: 0.96→1 Å /
RfactorNum. reflection
Rwork0.201 -
obs-18643

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