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- PDB-2a1u: Crystal structure of the human ETF E165betaA mutant -

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Basic information

Entry
Database: PDB / ID: 2a1u
TitleCrystal structure of the human ETF E165betaA mutant
Components
  • Electron transfer flavoprotein alpha-subunit, mitochondrial precursor
  • Electron transfer flavoprotein beta-subunit
KeywordsELECTRON TRANSPORT / electron transfer / mobile domain / conformational sampling
Function / homology
Function and homology information


electron transfer flavoprotein complex / fatty acid beta-oxidation using acyl-CoA dehydrogenase / amino acid catabolic process / Respiratory electron transport / Protein methylation / respiratory electron transport chain / flavin adenine dinucleotide binding / electron transfer activity / oxidoreductase activity / mitochondrial matrix / mitochondrion
Similarity search - Function
Electron transfer flavoprotein, beta-subunit, conserved site / Electron transfer flavoprotein subunit alpha, conserved site / Electron transfer flavoprotein alpha-subunit signature. / Electron transfer flavoprotein beta-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein domain / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal ...Electron transfer flavoprotein, beta-subunit, conserved site / Electron transfer flavoprotein subunit alpha, conserved site / Electron transfer flavoprotein alpha-subunit signature. / Electron transfer flavoprotein beta-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein domain / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain / Electron transfer flavoprotein domain / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Electron transfer flavoprotein subunit alpha, mitochondrial / Electron transfer flavoprotein subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsToogood, H.S. / Van Thiel, A. / Scrutton, N.S. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Stabilization of Non-productive Conformations Underpins Rapid Electron Transfer to Electron-transferring Flavoprotein
Authors: Toogood, H.S. / van Thiel, A. / Scrutton, N.S. / Leys, D.
History
DepositionJun 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Electron transfer flavoprotein alpha-subunit, mitochondrial precursor
B: Electron transfer flavoprotein beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0824
Polymers62,9492
Non-polymers1,1332
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-44 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.086, 62.869, 174.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Electron transfer flavoprotein alpha-subunit, mitochondrial precursor / Alpha-ETF


Mass: 35121.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pK18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P13804
#2: Protein Electron transfer flavoprotein beta-subunit / Beta-ETF


Mass: 27827.611 Da / Num. of mol.: 1 / Mutation: E165betaA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pK18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P38117
#3: 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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.9 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG2000MME, 0.1 magnesium sulphate, 0.1M cacodylic acid, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2005
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 28046 / Num. obs: 28046 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.4 / % possible all: 62.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFV

1efv


Resolution: 2.11→18.74 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.696 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.283 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24695 1401 5 %RANDOM
Rwork0.17918 ---
all0.1826 26508 --
obs0.1826 26508 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.891 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.11→18.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 76 270 4532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4242.0095893
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89925.306147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01115741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9011520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.22050
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23021
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2316
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8031.52917
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22124567
X-RAY DIFFRACTIONr_scbond_it1.89231612
X-RAY DIFFRACTIONr_scangle_it3.0964.51325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.164 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 98 -
Rwork0.218 1623 -
obs--100 %

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