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- PDB-2gmh: Structure of Porcine Electron Transfer Flavoprotein-Ubiquinone Ox... -

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Entry
Database: PDB / ID: 2gmh
TitleStructure of Porcine Electron Transfer Flavoprotein-Ubiquinone Oxidoreductase in Complexed with Ubiquinone
ComponentsElectron transfer flavoprotein-ubiquinone oxidoreductase
KeywordsOXIDOREDUCTASE / Electron-Transfer / Oxidoreductase / Flavoprotein / Ubiquinone
Function / homologyNAD(P)-binding Rossmann-like domain / Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Electron transfer flavoprotein-ubiquinone oxidoreductase / FAD/NAD(P)-binding domain superfamily / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / oxidoreductase activity, oxidizing metal ions with flavin as acceptor / electron-transferring-flavoprotein dehydrogenase / electron-transferring-flavoprotein dehydrogenase activity / integral component of mitochondrial inner membrane ...NAD(P)-binding Rossmann-like domain / Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Electron transfer flavoprotein-ubiquinone oxidoreductase / FAD/NAD(P)-binding domain superfamily / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / oxidoreductase activity, oxidizing metal ions with flavin as acceptor / electron-transferring-flavoprotein dehydrogenase / electron-transferring-flavoprotein dehydrogenase activity / integral component of mitochondrial inner membrane / iron-sulfur cluster binding / ubiquinone binding / electron transport chain / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / flavin adenine dinucleotide binding / response to oxidative stress / electron transfer activity / oxidoreductase activity / mitochondrion / membrane / metal ion binding / Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial
Function and homology information
Specimen sourceSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.5 Å resolution
AuthorsZhang, J. / Frerman, F.E. / Kim, J.-J.P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
Authors: Zhang, J. / Frerman, F.E. / Kim, J.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 6, 2006 / Release: Oct 17, 2006
RevisionDateData content typeGroupProviderType
1.0Oct 17, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Electron transfer flavoprotein-ubiquinone oxidoreductase
B: Electron transfer flavoprotein-ubiquinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,61022
Polyers129,8532
Non-polymers4,75720
Water6,648369
1
A: Electron transfer flavoprotein-ubiquinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,69716
Polyers64,9271
Non-polymers2,77015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Electron transfer flavoprotein-ubiquinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9136
Polyers64,9271
Non-polymers1,9865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)154.322, 154.322, 128.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP 4 21 2

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Electron transfer flavoprotein-ubiquinone oxidoreductase / ETF-QO / ETF-ubiquinone oxidoreductase / ETF dehydrogenase / Electron-transferring- flavoprotein dehydrogenase / Fragment


Mass: 64926.582 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / Genus: Sus
References: UniProt: P55931, electron-transferring-flavoprotein dehydrogenase

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Non-polymers , 7 types, 389 molecules

#2: Chemical ChemComp-BHG / 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL


Mass: 264.315 Da / Num. of mol.: 3 / Formula: C12H24O6
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Formula: Fe4S4 / Iron–sulfur cluster
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#6: Chemical ChemComp-UQ5 / 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE


Mass: 522.758 Da / Num. of mol.: 2 / Formula: C34H50O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Formula: C2H6O2 / Ethylene glycol
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Formula: H2O / Water

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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: 2.94 / Density percent sol: 58.23 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEGMME 2000, Sodium Chloride, Ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 14-BM-C / Synchrotron site: APS / Beamline: 14-BM-C / Wavelength: 1.0, 1.7389, 1.7426, 1.6000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Nov 21, 1999
RadiationMonochromator: graphite / Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
11.01.0
21.73891.0
31.74261.0
41.60001.0
ReflectionB iso Wilson estimate: 37.1 Å2 / D resolution high: 2.5 Å / D resolution low: 29.67 Å / Number obs: 53508 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rsym value: 0.065 / NetI over sigmaI: 35.3 / Redundancy: 11.9 % / Percent possible obs: 98.7
Reflection shellHighest resolution: 2.5 Å / Lowest resolution: 2.54 Å / MeanI over sigI obs: 7.6 / Number unique all: 2590 / Rsym value: 0.649 / Redundancy: 4.5 % / Percent possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefineMethod to determine structure: MAD / Details: BULK SOLVENT MODEL USED / R Free selection details: RANDOM / Data cutoff high absF: 297102.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 35.225 / Solvent model param ksol: 0.303289
Displacement parametersB iso mean: 47.9 Å2 / Aniso B11: -4.14 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -4.14 Å2 / Aniso B23: 0 Å2 / Aniso B33: 8.28 Å2
Least-squares processR factor R free: 0.254 / R factor R free error: 0.004 / R factor R work: 0.221 / R factor obs: 0.221 / Highest resolution: 2.5 Å / Lowest resolution: 29.67 Å / Number reflection R free: 4358 / Number reflection all: 53508 / Number reflection obs: 53508 / Percent reflection R free: 8.1 / Percent reflection obs: 98.7
Refine analyzeLuzzati coordinate error free: 0.38 Å / Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 29.67 Å / Luzzati sigma a free: 0.48 Å / Luzzati sigma a obs: 0.42 Å
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 29.67 Å
Number of atoms included #LASTProtein: 9089 / Nucleic acid: 0 / Ligand: 293 / Solvent: 369 / Total: 9751
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg3.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d3.81
X-RAY DIFFRACTIONc_mcbond_it1.201.50
X-RAY DIFFRACTIONc_mcangle_it1.922.00
X-RAY DIFFRACTIONc_scbond_it1.792.00
X-RAY DIFFRACTIONc_scangle_it2.532.50
Refine LS shellHighest resolution: 2.5 Å / R factor R free: 0.39 / R factor R free error: 0.019 / R factor R work: 0.368 / Lowest resolution: 2.59 Å / Number reflection R free: 428 / Number reflection R work: 4698 / Number reflection obs: 4699 / Total number of bins used: 10 / Percent reflection R free: 8.3 / Percent reflection obs: 96.2
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4prosth2.parprosth2.top
X-RAY DIFFRACTION5u10.paru10.top

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