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

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Basic information

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 / Flavoprotein / Ubiquinone
Function / homology
Function and homology information


electron-transferring-flavoprotein dehydrogenase / electron-transferring-flavoprotein dehydrogenase activity / ubiquinone binding / iron-sulfur cluster binding / electron transport chain / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / electron transfer activity ...electron-transferring-flavoprotein dehydrogenase / electron-transferring-flavoprotein dehydrogenase activity / ubiquinone binding / iron-sulfur cluster binding / electron transport chain / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / electron transfer activity / oxidoreductase activity / mitochondrion / membrane / metal ion binding
Similarity search - Function
D-Amino Acid Oxidase; Chain A, domain 2 - #90 / : / Electron transfer flavoprotein-ubiquinone oxidoreductase / : / ETF-QO, ubiquinone-binding / Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S / NAD(P)-binding Rossmann-like domain / Alpha-Beta Plaits - #20 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain ...D-Amino Acid Oxidase; Chain A, domain 2 - #90 / : / Electron transfer flavoprotein-ubiquinone oxidoreductase / : / ETF-QO, ubiquinone-binding / Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S / NAD(P)-binding Rossmann-like domain / Alpha-Beta Plaits - #20 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
hexyl beta-D-galactopyranoside / FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Chem-UQ5 / Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
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.
History
DepositionApr 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Electron transfer flavoprotein-ubiquinone oxidoreductase
B: Electron transfer flavoprotein-ubiquinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,61022
Polymers129,8532
Non-polymers4,75720
Water6,648369
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A: Electron transfer flavoprotein-ubiquinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,69716
Polymers64,9271
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
Polymers64,9271
Non-polymers1,9865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP4212

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Components

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Protein / Sugars , 2 types, 5 molecules AB

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


Mass: 64926.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P55931, electron-transferring-flavoprotein dehydrogenase
#2: Sugar ChemComp-BHG / hexyl beta-D-galactopyranoside / 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / hexyl beta-D-galactoside / hexyl D-galactoside / hexyl galactoside


Type: D-saccharide / Mass: 264.315 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H24O6

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Non-polymers , 6 types, 386 molecules

#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / 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 / Source method: obtained synthetically / Formula: C34H50O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 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 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.0, 1.7389, 1.7426, 1.6000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 1999
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.73891
31.74261
41.61
ReflectionResolution: 2.5→29.67 Å / Num. obs: 53508 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 37.1 Å2 / Rsym value: 0.065 / Net I/σ(I): 35.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 7.6 / Num. unique all: 2590 / Rsym value: 0.649 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 297102.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4358 8.1 %RANDOM
Rwork0.221 ---
obs0.221 53508 98.7 %-
all-53508 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.225 Å2 / ksol: 0.303289 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å20 Å20 Å2
2---4.14 Å20 Å2
3---8.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-29.67 Å
Luzzati sigma a0.48 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9089 0 293 369 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_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.39 428 8.3 %
Rwork0.368 4698 -
obs-4699 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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