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- PDB-5ow0: Crystal structure of an electron transfer flavoprotein from Geoba... -

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Basic information

Entry
Database: PDB / ID: 5ow0
TitleCrystal structure of an electron transfer flavoprotein from Geobacter metallireducens
Components
  • Electron transfer flavoprotein, alpha subunit
  • Electron transfer flavoprotein, beta subunit
KeywordsELECTRON TRANSPORT / anaerobic / toluene metabolism / FAD / AMP / flavoprotein
Function / homology
Function and homology information


flavin adenine dinucleotide binding / electron transfer activity
Similarity search - Function
Electron transfer flavoprotein, beta subunit / 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 ...Electron transfer flavoprotein, beta subunit / 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 / 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, alpha subunit / Electron transfer flavoprotein, beta subunit
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsEssen, L.-O. / Vogt, M.S. / Heider, J. / Koelzer, S. / Peschke, P. / Chowdhury, N.P. / Schuehle, K. / Kleinsorge, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB987/E09 Germany
CitationJournal: J.Bacteriol. / Year: 2019
Title: Structural and functional characterization of an electron transfer flavoprotein involved in toluene degradation in strictly anaerobic bacteria.
Authors: Vogt, M.S. / Schuhle, K. / Kolzer, S. / Peschke, P. / Chowdhury, N.P. / Kleinsorge, D. / Buckel, W. / Essen, L.O. / Heider, J.
History
DepositionAug 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,6314
Polymers58,4982
Non-polymers1,1332
Water13,295738
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-57 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.730, 72.750, 133.881
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, beta subunit


Mass: 27615.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: etfB-5, Gmet_1525 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VG5
#2: Protein Electron transfer flavoprotein, alpha subunit


Mass: 30881.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: etfA-5, Gmet_1526 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VG4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Mother liquor: 15% (w/v) PEG 3350, 0.1 M HEPES, pH 7.5 mixed equal volumes of 10 mg/ml EtfAB in 300 mM NaCl, 20 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.7→44.63 Å / Num. obs: 59506 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 17.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 5846 / CC1/2: 0.918 / Rpim(I) all: 0.25 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→43.736 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.68
RfactorNum. reflection% reflection
Rfree0.1674 2970 5 %
Rwork0.1364 --
obs0.138 59434 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 76 738 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154252
X-RAY DIFFRACTIONf_angle_d1.5395790
X-RAY DIFFRACTIONf_dihedral_angle_d14.5241606
X-RAY DIFFRACTIONf_chiral_restr0.066690
X-RAY DIFFRACTIONf_plane_restr0.008736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72790.21341620.1962624X-RAY DIFFRACTION99
1.7279-1.75770.24831070.17632676X-RAY DIFFRACTION99
1.7577-1.78960.19891390.17082636X-RAY DIFFRACTION99
1.7896-1.82410.19121220.16662684X-RAY DIFFRACTION99
1.8241-1.86130.18971410.15692645X-RAY DIFFRACTION100
1.8613-1.90180.19411610.15512627X-RAY DIFFRACTION99
1.9018-1.9460.15281340.14492655X-RAY DIFFRACTION100
1.946-1.99470.18921280.14282645X-RAY DIFFRACTION99
1.9947-2.04860.18571550.142641X-RAY DIFFRACTION100
2.0486-2.10890.16561340.13472692X-RAY DIFFRACTION100
2.1089-2.1770.15351370.13542676X-RAY DIFFRACTION100
2.177-2.25480.16321270.13082682X-RAY DIFFRACTION100
2.2548-2.3450.17991570.12942668X-RAY DIFFRACTION100
2.345-2.45170.15311270.13232683X-RAY DIFFRACTION100
2.4517-2.5810.18581430.14052702X-RAY DIFFRACTION100
2.581-2.74270.19491640.13932689X-RAY DIFFRACTION100
2.7427-2.95440.19211250.1442712X-RAY DIFFRACTION100
2.9544-3.25160.16221390.13852735X-RAY DIFFRACTION100
3.2516-3.72190.15721530.12472718X-RAY DIFFRACTION100
3.7219-4.68840.12881330.11082784X-RAY DIFFRACTION100
4.6884-43.75010.15451820.13672883X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3551-1.98590.04554.606-0.28421.12130.05660.10480.0206-0.3331-0.05130.0623-0.0414-0.11160.00160.125-0.0187-0.03050.1289-0.0060.084931.819930.996374.5179
24.6039-6.0522-3.12048.28943.61663.35630.1221-0.1540.2708-0.35360.0743-0.4339-0.09140.2333-0.17030.1704-0.01660.0310.1599-0.01740.175850.058424.616176.2034
31.04470.12880.02361.39640.15091.2547-0.02540.0224-0.0983-0.04740.016-0.02730.11020.05520.00650.12730.00340.01350.1089-0.00590.132640.460219.818281.4183
43.6094-0.46561.44688.46132.4244.1467-0.1261-0.11160.01550.26620.1435-0.325-0.00280.2134-0.02740.0966-0.00310.02060.18290.01020.09851.487926.09591.7234
51.48870.3046-1.6250.5397-0.76292.387-0.08980.3419-0.0361-0.30860.1232-0.09540.1228-0.0823-0.05080.16910.05710.00190.1657-0.00660.195544.57922.960967.9239
61.02981.4205-0.20194.6344-0.62260.4239-0.02610.03890.1265-0.1590.06070.1394-0.0244-0.061-0.03690.120.00810.00790.1524-0.00060.114232.206153.363181.9087
71.2548-0.56610.43520.9782-0.53251.9217-0.1387-0.1842-0.02960.18250.118-0.0005-0.0382-0.00350.02090.14790.00850.00760.14340.01260.123935.040530.5555103.8824
81.5873-2.55921.01135.1518-1.83310.6883-0.3411-0.06390.39560.71050.2312-1.0697-0.36640.1470.09370.2956-0.0206-0.07780.2627-0.05040.283353.455541.78795.4413
91.59880.1109-0.09832.4951-0.51051.16780.02290.00470.0735-0.04620.0261-0.1872-0.06360.0972-0.040.1072-0.01260.0060.0979-0.01870.091944.656853.279480.5803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'B' and (resid 37 through 53 )
3X-RAY DIFFRACTION3chain 'B' and (resid 54 through 157 )
4X-RAY DIFFRACTION4chain 'B' and (resid 158 through 175 )
5X-RAY DIFFRACTION5chain 'B' and (resid 176 through 203 )
6X-RAY DIFFRACTION6chain 'B' and (resid 204 through 251 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 157 )
8X-RAY DIFFRACTION8chain 'A' and (resid 158 through 177 )
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 294 )

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