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- PDB-7tnv: Crystal Structure Of Human NADH-Cytochrome B5 Reductase T117S Mutant -

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Basic information

Entry
Database: PDB / ID: 7tnv
TitleCrystal Structure Of Human NADH-Cytochrome B5 Reductase T117S Mutant
ComponentsNADH-cytochrome b5 reductase 3 soluble form
KeywordsOXIDOREDUCTASE / FAD / B5R / Reductase / T117S
Function / homology
Function and homology information


nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / AMP binding / cholesterol biosynthetic process / hemoglobin complex / nitric oxide biosynthetic process ...nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / AMP binding / cholesterol biosynthetic process / hemoglobin complex / nitric oxide biosynthetic process / FAD binding / lipid droplet / mitochondrial membrane / ADP binding / NAD binding / azurophil granule lumen / mitochondrial outer membrane / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / extracellular region / membrane / cytosol / cytoplasm
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZheng, A. / Thibodeau, P.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122091 United States
CitationJournal: to be published
Title: Structure Of wild-type Human NADH-Cytochrome B5 Reductase and mutants
Authors: Zheng, A. / Thibodeau, P.H.
History
DepositionJan 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,9232
Polymers31,1381
Non-polymers7861
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.530, 65.530, 71.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein NADH-cytochrome b5 reductase 3 soluble form


Mass: 31137.947 Da / Num. of mol.: 1 / Mutation: T117S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00387
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 7.8, PEG 4K 10%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.93→46.34 Å / Num. obs: 22991 / % possible obs: 99.8 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.073 / Net I/av σ(I): 23.58 / Net I/σ(I): 21.8
Reflection shellResolution: 1.93→1.98 Å / Mean I/σ(I) obs: 2.55 / Num. unique obs: 1640 / CC1/2: 0.809 / Rrim(I) all: 1.602

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1umk

1umk


Resolution: 1.93→46.34 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 2011 8.76 %
Rwork0.1811 20953 -
obs0.1829 22964 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.03 Å2
Refinement stepCycle: LAST / Resolution: 1.93→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 53 271 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292275
X-RAY DIFFRACTIONf_angle_d0.6153098
X-RAY DIFFRACTIONf_chiral_restr0.0489332
X-RAY DIFFRACTIONf_plane_restr0.0053396
X-RAY DIFFRACTIONf_dihedral_angle_d9.2183300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.38711360.37671444X-RAY DIFFRACTION97.23
1.98-2.030.30041440.27451483X-RAY DIFFRACTION99.88
2.03-2.090.27271420.21961489X-RAY DIFFRACTION100
2.09-2.160.24461420.20271515X-RAY DIFFRACTION100
2.16-2.230.23041420.20051474X-RAY DIFFRACTION100
2.23-2.320.2341420.21861517X-RAY DIFFRACTION100
2.32-2.430.25161410.21421486X-RAY DIFFRACTION100
2.43-2.560.26871470.19751504X-RAY DIFFRACTION100
2.56-2.720.22851430.20331507X-RAY DIFFRACTION99.94
2.72-2.930.21081430.20351483X-RAY DIFFRACTION99.94
2.93-3.220.21541470.18541491X-RAY DIFFRACTION99.94
3.22-3.690.17921460.16081515X-RAY DIFFRACTION100
3.69-4.640.13681470.13821513X-RAY DIFFRACTION100
4.64-46.340.17141490.15921532X-RAY DIFFRACTION99.82

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