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- PDB-2eix: The Structure of Physarum polycephalum cytochrome b5 reductase -

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Basic information

Entry
Database: PDB / ID: 2eix
TitleThe Structure of Physarum polycephalum cytochrome b5 reductase
ComponentsNADH-cytochrome b5 reductase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / FAD-BINDING DOMAIN / NADH-BINDING
Function / homology
Function and homology information


cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / nucleotide binding / mitochondrion / membrane
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 / IODIDE ION / NADH-cytochrome b5 reductase
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKim, S.W. / Suga, M. / Ogasahara, K. / Ikegami, T. / Minami, Y. / Yubisui, T. / Tsukihara, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of Physarum polycephalum cytochrome b5 reductase at 1.56 A resolution.
Authors: Kim, S. / Suga, M. / Ogasahara, K. / Ikegami, T. / Minami, Y. / Yubisui, T. / Tsukihara, T.
History
DepositionMar 14, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: NADH-cytochrome b5 reductase
B: NADH-cytochrome b5 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,87512
Polymers55,5662
Non-polymers2,30910
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-56 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.084, 136.369, 45.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NADH-cytochrome b5 reductase


Mass: 27783.141 Da / Num. of mol.: 2 / Fragment: residues 39-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Plasmid: PUC13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1HA49, cytochrome-b5 reductase

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Non-polymers , 5 types, 484 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 4000, 50mM ADA, 200mM Sodium iodide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.56→43.355 Å / Num. all: 88222 / Num. obs: 83782 / Redundancy: 7.1 % / Net I/σ(I): 28.5
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMK

1umk


Resolution: 1.56→43.355 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.226 4185 RANDOM
Rwork0.18 --
all0.184 --
obs-83782 -
Refinement stepCycle: LAST / Resolution: 1.56→43.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 124 474 4498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.02
X-RAY DIFFRACTIONr_angle_refined_deg2
LS refinement shellResolution: 1.56→1.62 Å /
RfactorNum. reflection
Rfree0.226 4185
Rwork0.184 -

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