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- PDB-6mv1: 2.15A resolution structure of the CS-b5R domains of human Ncb5or ... -

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Basic information

Entry
Database: PDB / ID: 6mv1
Title2.15A resolution structure of the CS-b5R domains of human Ncb5or (NAD+ form)
ComponentsCytochrome b5 reductase 4
KeywordsOXIDOREDUCTASE / NCB5OR / ELECTRON TRANSFER / REDOX / HEME / ENDOPLASMIC RETICULUM / FAD / FLAVOPROTEIN / IRON / METAL-BINDING / NAD
Function / homology
Function and homology information


cytochrome-b5 reductase / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / detection of oxygen / cytochrome-b5 reductase activity, acting on NAD(P)H / cell development / NAD(P)H oxidase H2O2-forming activity / bicarbonate transport / insulin secretion / superoxide metabolic process / reactive oxygen species metabolic process ...cytochrome-b5 reductase / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / detection of oxygen / cytochrome-b5 reductase activity, acting on NAD(P)H / cell development / NAD(P)H oxidase H2O2-forming activity / bicarbonate transport / insulin secretion / superoxide metabolic process / reactive oxygen species metabolic process / generation of precursor metabolites and energy / Erythrocytes take up carbon dioxide and release oxygen / glucose homeostasis / response to antibiotic / heme binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / metal ion binding / cytosol
Similarity search - Function
Cytochrome b5 reductase 4, p23 domain / CS domain / CS domain / CS domain profile. / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain ...Cytochrome b5 reductase 4, p23 domain / CS domain / CS domain / CS domain profile. / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / HSP20-like chaperone / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Cytochrome b5 reductase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Benson, D.R. / Cooper, A. / Gao, P. / Zhu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of the naturally fused CS and cytochrome b5reductase (b5R) domains of Ncb5or reveal an expanded CS fold, extensive CS-b5R interactions and productive binding of the NAD(P)+nicotinamide ring.
Authors: Benson, D.R. / Lovell, S. / Mehzabeen, N. / Galeva, N. / Cooper, A. / Gao, P. / Battaile, K.P. / Zhu, H.
History
DepositionOct 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Cytochrome b5 reductase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5683
Polymers42,1201
Non-polymers1,4492
Water2,378132
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)56.137, 68.628, 57.598
Angle α, β, γ (deg.)90.000, 97.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome b5 reductase 4 / Flavohemoprotein b5/b5R / b5+b5R / N-terminal cytochrome b5 and cytochrome b5 oxidoreductase domain- ...Flavohemoprotein b5/b5R / b5+b5R / N-terminal cytochrome b5 and cytochrome b5 oxidoreductase domain-containing protein / cb5/cb5R


Mass: 42119.504 Da / Num. of mol.: 1 / Fragment: CS-b5R domains (residues 164-521)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYB5R4, NCB5OR / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS-RARE / References: UniProt: Q7L1T6, 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.61 Å3/Da / Density % sol: 52.9 % / Mosaicity: 0.15 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% (w/v) PEG 6000, 0.1 M Hepes, 0.2 M NDSB-201

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→43.9 Å / Num. obs: 23683 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.8 / Num. measured all: 80292 / Scaling rejects: 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.15-2.223.30.67920670.776199.7
8.86-43.93.30.0263590.999198

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.94 Å43.9 Å
Translation5.94 Å43.9 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EIX

2eix


Resolution: 2.15→34.314 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 27.44
RfactorNum. reflection% reflection
Rfree0.2301 1189 5.03 %
Rwork0.1828 --
obs0.1852 23654 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.73 Å2 / Biso mean: 38.2472 Å2 / Biso min: 18.56 Å2
Refinement stepCycle: final / Resolution: 2.15→34.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 97 132 2982
Biso mean--40.15 40.88 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092929
X-RAY DIFFRACTIONf_angle_d1.084015
X-RAY DIFFRACTIONf_chiral_restr0.059471
X-RAY DIFFRACTIONf_plane_restr0.007489
X-RAY DIFFRACTIONf_dihedral_angle_d12.7291716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1501-2.24790.30451300.261328202950100
2.2479-2.36640.331410.241327882929100
2.3664-2.51460.26031520.214627812933100
2.5146-2.70870.26191910.204227622953100
2.7087-2.98110.27921370.204928272964100
2.9811-3.41220.29621450.183528142959100
3.4122-4.29760.18851440.153228042948100
4.2976-34.31840.15791490.1582869301899

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