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- PDB-5ol2: The electron transferring flavoprotein/butyryl-CoA dehydrogenase ... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5ol2
TitleThe electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile
Components
  • (Electron transfer flavoprotein ...) x 2
  • Acyl-CoA dehydrogenase
KeywordsFLAVOPROTEIN / Flavin based electron bifurcation / Bioenergetics / electron transferring flavoprotein / acyl-CoA dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / short-chain acyl-CoA dehydrogenase / short-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / flavin adenine dinucleotide binding / electron transfer activity / nucleotide binding / metal ion binding
Similarity search - Function
Electron transfer flavoprotein subunit alpha, conserved site / Electron transfer flavoprotein alpha-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein domain / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain ...Electron transfer flavoprotein subunit alpha, conserved site / Electron transfer flavoprotein alpha-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein domain / Electron transfer flavoprotein alpha subunit/FixB / 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 / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / TPP-binding domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / DHS-like NAD/FAD-binding domain superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Up-down Bundle / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A PERSULFIDE / FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase / Electron transfer flavoprotein small subunit / Electron transfer flavoprotein large subunit / Electron transfer flavoprotein subunit beta / Electron transfer flavoprotein subunit alpha / Butyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsDemmer, J.K. / Chowdhury, N.P. / Selmer, T. / Ermler, U. / Buckel, W.
Funding support Germany, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation Germany
SYNMIKRO Germany
CitationJournal: Nat Commun / Year: 2017
Title: The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile.
Authors: Demmer, J.K. / Pal Chowdhury, N. / Selmer, T. / Ermler, U. / Buckel, W.
History
DepositionJul 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Electron transfer flavoprotein large subunit
B: Electron transfer flavoprotein small subunit
C: Acyl-CoA dehydrogenase
D: Electron transfer flavoprotein large subunit
E: Electron transfer flavoprotein small subunit
F: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,08219
Polymers210,5696
Non-polymers6,51313
Water00
1
A: Electron transfer flavoprotein large subunit
B: Electron transfer flavoprotein small subunit
C: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5219
Polymers105,2853
Non-polymers3,2366
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13150 Å2
ΔGint-83 kcal/mol
Surface area40780 Å2
MethodPISA
2
D: Electron transfer flavoprotein large subunit
E: Electron transfer flavoprotein small subunit
F: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,56110
Polymers105,2853
Non-polymers3,2767
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-89 kcal/mol
Surface area40860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.060, 177.060, 493.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain C
22chain F
13chain B
23chain E

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYchain AAA1 - 3311 - 331
21GLYGLYchain DDD1 - 3311 - 331
12LYSLYSchain CCC1 - 3781 - 378
22LYSLYSchain FFF1 - 3781 - 378
13ILEILEchain BBB6 - 2651 - 260
23ILEILEchain EEE6 - 2651 - 260

NCS ensembles :
ID
1
2
3

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Components

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Electron transfer flavoprotein ... , 2 types, 4 molecules ADBE

#1: Protein Electron transfer flavoprotein large subunit / Electron transfer flavoprotein subunit alpha


Mass: 35587.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: etfA, etfA_4, BN1095_140023, BN1096_550022, BN1097_530021, SAMEA3374989_03962, SAMEA3375004_04103, SAMEA3375059_03747
Production host: Escherichia coli (E. coli) / References: UniProt: A0A031WK27, UniProt: A0A125V455*PLUS
#2: Protein Electron transfer flavoprotein small subunit / Electron transfer flavoprotein subunit beta / Electron transfer flavoproteins subunit beta


Mass: 28346.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: etfB, etfB_3, etfB_4, BN1095_140022, BN1096_550021, BN1097_530020, IM33_05895, SAMEA3374973_01501, SAMEA3374989_03963, SAMEA3375004_04104, SAMEA3375059_03748
Production host: Escherichia coli (E. coli) / References: UniProt: A0A031WJM1, UniProt: A0A125V3V6*PLUS

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Protein , 1 types, 2 molecules CF

#3: Protein Acyl-CoA dehydrogenase / Acyl-CoA dehydrogenase / short-chain specific / Butyryl-CoA dehydrogenase


Mass: 41350.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: acdA, bcd, BN1095_140021, BN1096_550020, BN1097_530019, IM33_05890, SAMEA3374973_01502, SAMEA3374989_03964, SAMEA3375004_04105, SAMEA3375059_03749
Production host: Escherichia coli (E. coli)
References: UniProt: A0A031WJ47, UniProt: A0A125V4E7*PLUS, short-chain acyl-CoA dehydrogenase, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors

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Non-polymers , 3 types, 13 molecules

#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-COS / COENZYME A PERSULFIDE


Mass: 799.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S2

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Details

Has protein modificationN

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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: 4.59 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M calcium acetate; 14 % (v/v) PEG 400; 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.866 Å / Num. obs: 70563 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 104.56 Å2 / Rsym value: 0.143 / Net I/σ(I): 11.1
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 0.9 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPU and 4L1F

4kpu

4l1f


Resolution: 3.1→48.866 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.95 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2595 3479 4.98 %
Rwork0.2088 66331 -
obs0.2113 69810 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 373.66 Å2 / Biso mean: 130.8201 Å2 / Biso min: 72.55 Å2
Refinement stepCycle: final / Resolution: 3.1→48.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14744 0 421 0 15165
Biso mean--150.75 --
Num. residues----1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01915415
X-RAY DIFFRACTIONf_angle_d1.89620888
X-RAY DIFFRACTIONf_chiral_restr0.0972392
X-RAY DIFFRACTIONf_plane_restr0.0112622
X-RAY DIFFRACTIONf_dihedral_angle_d7.7969188
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3100X-RAY DIFFRACTION6.936TORSIONAL
12D3100X-RAY DIFFRACTION6.936TORSIONAL
21C3654X-RAY DIFFRACTION6.936TORSIONAL
22F3654X-RAY DIFFRACTION6.936TORSIONAL
31B2448X-RAY DIFFRACTION6.936TORSIONAL
32E2448X-RAY DIFFRACTION6.936TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.14250.52331220.51382531265395
3.1425-3.18730.55361180.46612584270296
3.1873-3.23490.47911330.42622538267195
3.2349-3.28540.50221460.41222586273297
3.2854-3.33930.42811290.40142608273797
3.3393-3.39690.48611570.36932556271397
3.3969-3.45860.40111490.33052590273997
3.4586-3.52510.35151330.30122619275297
3.5251-3.59710.34011310.28612617274897
3.5971-3.67520.29481250.27242613273897
3.6752-3.76070.29091610.26432622278399
3.7607-3.85470.32181120.24382660277298
3.8547-3.95890.27761310.22732651278298
3.9589-4.07530.25741300.21892657278799
4.0753-4.20680.25761330.20282650278398
4.2068-4.35710.25361370.18882641277898
4.3571-4.53140.19971470.16982675282298
4.5314-4.73750.23751430.16122654279799
4.7375-4.9870.19111510.1622680283199
4.987-5.29910.21021460.16062704285099
5.2991-5.70770.24441330.165327462879100
5.7077-6.2810.22141580.166127212879100
6.281-7.18740.22781480.17627432891100
7.1874-9.0460.20421400.158228032943100
9.046-48.8720.23761660.19222882304898
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)
14.5797-1.0289-0.58681.99420.64033.1169-0.0877-0.0789-0.7055-0.2161-0.01120.22020.6388-0.23640.10181.6433-0.0990.02971.050.03471.0393-93.8201-60.4995-20.249
28.01480.38011.30352.91920.84367.5503-0.07430.3642-0.8986-0.26880.5052-0.3190.61420.5546-0.38271.6513-0.1711-0.0090.8364-0.0751.1016-85.9009-48.260514.6302
32.40911.39291.64744.161-1.45723.4172-0.08050.00660.27960.00080.15710.4107-0.9544-0.0078-0.10041.5363-0.01530.00361.04-0.18851.1203-85.977-29.6181-16.6
43.8975-1.0571.82323.7339-0.35592.0305-0.1965-0.0468-0.2168-0.2627-0.05120.02390.49280.14090.26851.55750.11760.09811.252-0.13141.0095-81.7356-43.3696-23.3158
52.3441.9520.50376.20363.46843.98830.2483-0.18140.54960.277-0.49320.4196-0.74930.31530.1281.6177-0.00040.05911.3217-0.12411.1331-78.3667-23.4228-17.5215
68.26915.2891-5.40753.7645-4.45036.0736-0.15181.2667-0.1236-1.44990.71470.96440.4841-0.3151-0.68321.42690.2354-0.17961.2687-0.15940.9549-97.246-34.315-34.6747
71.6982-1.62812.35152.0827-2.68323.52070.6059-0.11670.0261-0.31290.05440.34411.7408-0.2784-0.64771.49780.06310.02941.1695-0.0441.2781-101.141-51.76183.8745
86.2257-0.38694.96561.1633-2.3718.3233-0.1082-0.32940.3335-0.0705-0.0202-0.32730.823-0.22990.08631.42780.10270.10750.9571-0.17461.1423-73.8931-20.07080.0436
92.5961-0.042-0.05181.35170.11972.5466-0.120.43460.0404-0.41170.1441-0.21120.13940.4518-0.01631.1248-0.09420.0720.9711-0.04130.8439-68.7326-6.14096.394
101.4134-0.54340.85624.8758-1.25423.6571-0.0138-0.18820.1882-0.0889-0.0832-0.7225-0.12340.89220.0670.8797-0.11430.05591.76640.0140.9379-28.21945.460466.1265
111.603-1.4222.42231.1437-2.01173.64350.077-0.0217-0.7519-0.40730.67310.28791.41330.9182-0.72421.4713-0.0103-0.28681.94230.02071.2347-39.799-11.26340.569
123.01781.54952.13927.58841.7387.20720.31270.2623-0.57090.3747-0.1037-0.43960.43821.1427-0.20260.9704-0.1908-0.08072.00860.03361.1561-40.2613-2.740130.4926
133.09792.3054-1.47323.74441.1663.5259-0.14850.20170.2153-0.16670.31290.3826-0.367-1.1459-0.22251.01050.0567-0.18571.57720.06551.1315-59.2853-2.951962.3716
144.1316-0.3621.05878.6245-2.08414.19470.07490.0561-0.0835-0.3138-0.4477-0.62810.34660.70750.34581.03170.2094-0.10611.4365-0.03350.8723-45.5828-7.141369.1711
155.49821.07934.57492.30931.70164.4854-0.02250.29710.60060.32430.14180.19530.8228-0.1306-0.19651.2225-0.1609-0.11531.67340.10551.0726-65.5262-10.498863.3778
169.51236.0077-4.46417.0017-4.57543.04350.2659-1.04850.90861.09050.1102-0.228-0.00130.5469-0.45641.51540.2866-0.1641.7103-0.41431.3422-54.48188.700980.2517
174.9815-3.1868-4.5123.37773.78214.59360.1819-0.24051.0579-0.54060.9099-0.2426-0.8011.8488-1.04930.9786-0.26540.0431.2374-0.01161.1012-36.864211.746541.891
181.2373-0.1806-2.03623.6053.20387.61550.1153-0.5805-0.355-0.482-0.0633-0.03-0.3361.11710.010.92430.0696-0.19341.40130.06871.1079-68.8629-15.224645.7729
191.42760.11760.19022.33390.18112.0710.155-0.4153-0.26640.4353-0.1307-0.03180.47090.1505-0.02221.0607-0.1041-0.04891.12460.07820.8411-82.9493-19.992339.4648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 200 )A1 - 200
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 401 )A201 - 401
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 97 )B6 - 97
4X-RAY DIFFRACTION4chain 'B' and (resid 98 through 181 or resid 300 through 300 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 182 through 209 )B182 - 209
6X-RAY DIFFRACTION6chain 'B' and (resid 210 through 224 )B210 - 224
7X-RAY DIFFRACTION7chain 'B' and (resid 225 through 265 )B225 - 265
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 46 )C1 - 46
9X-RAY DIFFRACTION9chain 'C' and (resid 47 through 401 )C47 - 401
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 194 )D1 - 194
11X-RAY DIFFRACTION11chain 'D' and (resid 195 through 222 )D195 - 222
12X-RAY DIFFRACTION12chain 'D' and (resid 223 through 401 )D223 - 401
13X-RAY DIFFRACTION13chain 'E' and (resid 6 through 97 )E6 - 97
14X-RAY DIFFRACTION14chain 'E' and (resid 98 through 181 )E98 - 181
15X-RAY DIFFRACTION15chain 'E' and (resid 182 through 209 )E182 - 209
16X-RAY DIFFRACTION16chain 'E' and (resid 210 through 224 )E210 - 224
17X-RAY DIFFRACTION17chain 'E' and (resid 225 through 265 )E225 - 265
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 46)F1 - 46
19X-RAY DIFFRACTION19chain 'F' and (resid 47 through 401)F47 - 401

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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