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- PDB-9v6b: Neutron crystal structure of the oxidized form of b5R at pD 6.5 -

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Basic information

Entry
Database: PDB / ID: 9v6b
TitleNeutron crystal structure of the oxidized form of b5R at pD 6.5
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
FLAVIN-ADENINE DINUCLEOTIDE / NADH-cytochrome b5 reductase 3
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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)32,1197
Polymers30,8731
Non-polymers1,2466
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-7 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.628, 72.233, 85.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12% PEG 3350, 10mM potassium phosphate pD 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: JPARC MLF / Beamline: BL-03 / Type: J-PARC MLF BEAMLINE BL-03 / Wavelength: 2.6-4.4
DetectorType: iBIX / Detector: DIFFRACTOMETER / Date: May 24, 2014
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.61
24.41
ReflectionResolution: 1.6→20 Å / Num. obs: 38402 / % possible obs: 96.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 9.8 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.104 / Net I/σ(I): 6.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5355 / CC1/2: 0.758 / Rpim(I) all: 0.318 / % possible all: 93.1

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→16.44 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / Phase error: 17.32
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Neutron data
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 1971 5.13 %Select the same reflections as PDB code 5GV8
Rwork0.1789 36423 --
obs0.1801 38394 95.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.025691
NEUTRON DIFFRACTIONf_angle_d1.529712
NEUTRON DIFFRACTIONf_chiral_restr0.083371
NEUTRON DIFFRACTIONf_plane_restr0.011848
NEUTRON DIFFRACTIONf_dihedral_angle_d17.4421481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.26141400.20952471NEUTRON DIFFRACTION91
1.64-1.680.23371250.21242498NEUTRON DIFFRACTION93
1.68-1.730.22361520.19792506NEUTRON DIFFRACTION94
1.73-1.790.22981190.18912594NEUTRON DIFFRACTION96
1.79-1.850.23531500.18422582NEUTRON DIFFRACTION96
1.85-1.930.20211490.17332585NEUTRON DIFFRACTION96
1.93-2.020.1851290.16532615NEUTRON DIFFRACTION97
2.02-2.120.18481300.16052669NEUTRON DIFFRACTION97
2.12-2.250.17861360.15262670NEUTRON DIFFRACTION99
2.25-2.430.17351390.1522718NEUTRON DIFFRACTION99
2.43-2.670.17411760.16042625NEUTRON DIFFRACTION98
2.67-3.060.20831400.16982680NEUTRON DIFFRACTION97
3.06-3.840.1821570.17332661NEUTRON DIFFRACTION96
3.84-16.440.21351290.21312549NEUTRON DIFFRACTION87

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