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- PDB-1umk: The Structure of Human Erythrocyte NADH-cytochrome b5 Reductase -

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Basic information

Entry
Database: PDB / ID: 1umk
TitleThe Structure of Human Erythrocyte NADH-cytochrome b5 Reductase
ComponentsNADH-cytochrome b5 reductase
KeywordsOXIDOREDUCTASE / flavoprotein / beta barrel / FAD-binding domain / NADH-binding domain
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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.75 Å
AuthorsBando, S. / Takano, T. / Yubisui, T. / Shirabe, K. / Takeshita, M. / Horii, C. / Nakagawa, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of human erythrocyte NADH-cytochrome b5 reductase.
Authors: Bando, S. / Takano, T. / Yubisui, T. / Shirabe, K. / Takeshita, M. / Nakagawa, A.
History
DepositionOct 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: NADH-cytochrome b5 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0852
Polymers31,2991
Non-polymers7861
Water13,565753
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.869, 65.869, 76.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein NADH-cytochrome b5 reductase / B5R


Mass: 31299.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00387, cytochrome-b5 reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 753 / 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: 1.98 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: PEG 4000, potassium phosphate, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 27, 2002 / Details: OSMIC Multilayer Optic mirror
RadiationMonochromator: OSMIC mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→23.7 Å / Num. all: 32692 / Num. obs: 32639 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -4 / Redundancy: 5.2 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.05 / Net I/σ(I): 8.7
Reflection shellResolution: 1.75→1.795 Å / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 5.4 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.75→23.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.654 / SU ML: 0.055 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.116 / ESU R Free: 0.115
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 1651 5.1 %RANDOM
Rwork0.16512 ---
all0.1936 32639 --
obs0.16723 30988 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.098 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 53 753 2979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222291
X-RAY DIFFRACTIONr_angle_refined_deg1.0252.0023121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5395270
X-RAY DIFFRACTIONr_chiral_restr0.070.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021730
X-RAY DIFFRACTIONr_nbd_refined0.1830.21166
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2616
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.290
X-RAY DIFFRACTIONr_mcbond_it0.4711.51362
X-RAY DIFFRACTIONr_mcangle_it0.90122233
X-RAY DIFFRACTIONr_scbond_it1.2233929
X-RAY DIFFRACTIONr_scangle_it2.1844.5888
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.249 115
Rwork0.245 2261
obs-2261

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