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- PDB-7w0j: Acyl-CoA dehydrogenase, Tfu_1647 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7w0j
TitleAcyl-CoA dehydrogenase, Tfu_1647
ComponentsAcyl-CoA dehydrogenase
KeywordsFLAVOPROTEIN / dehydrogenase / FAD
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
Chem-875 / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsLiu, L.X. / Zhou, S.H. / Deng, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of an Acyl-CoA dehydrogenase Tfu_1647
Authors: Liu, L.X. / Zhou, S.H. / Deng, Y.
History
DepositionNov 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
G: Acyl-CoA dehydrogenase
F: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
C: Acyl-CoA dehydrogenase
E: Acyl-CoA dehydrogenase
H: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,66311
Polymers337,9828
Non-polymers1,6813
Water0
1
A: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
G: Acyl-CoA dehydrogenase
F: Acyl-CoA dehydrogenase


Theoretical massNumber of molelcules
Total (without water)168,9914
Polymers168,9914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16420 Å2
ΔGint-111 kcal/mol
Surface area47230 Å2
MethodPISA
2
B: Acyl-CoA dehydrogenase
C: Acyl-CoA dehydrogenase
E: Acyl-CoA dehydrogenase
H: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,6727
Polymers168,9914
Non-polymers1,6813
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18090 Å2
ΔGint-117 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.124, 88.908, 97.178
Angle α, β, γ (deg.)90.190, 91.930, 112.090
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 7 or resid 9...
21(chain B and (resid 6 through 7 or resid 9...
31(chain C and (resid 6 through 7 or resid 9...
41(chain D and (resid 6 through 7 or resid 9...
51(chain E and (resid 6 through 7 or resid 9...
61(chain F and (resid 6 through 7 or resid 9...
71(chain G and (resid 6 through 7 or resid 9...
81(chain H and (resid 6 through 7 or resid 9...
12(chain E and 401)
22(chain E and 402)
32(chain H and 401)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 7 or resid 9...A6 - 7
121(chain A and (resid 6 through 7 or resid 9...A9 - 11
131(chain A and (resid 6 through 7 or resid 9...A13 - 17
141(chain A and (resid 6 through 7 or resid 9...A39
151(chain A and (resid 6 through 7 or resid 9...A407
161(chain A and (resid 6 through 7 or resid 9...A6 - 384
171(chain A and (resid 6 through 7 or resid 9...A6 - 384
181(chain A and (resid 6 through 7 or resid 9...A6 - 384
191(chain A and (resid 6 through 7 or resid 9...A6 - 384
1101(chain A and (resid 6 through 7 or resid 9...A6 - 384
1111(chain A and (resid 6 through 7 or resid 9...A6 - 384
211(chain B and (resid 6 through 7 or resid 9...B6 - 7
221(chain B and (resid 6 through 7 or resid 9...B9 - 11
231(chain B and (resid 6 through 7 or resid 9...B0
241(chain B and (resid 6 through 7 or resid 9...B2
251(chain B and (resid 6 through 7 or resid 9...B39
261(chain B and (resid 6 through 7 or resid 9...B5 - 384
271(chain B and (resid 6 through 7 or resid 9...B5 - 384
281(chain B and (resid 6 through 7 or resid 9...B5 - 384
291(chain B and (resid 6 through 7 or resid 9...B5 - 384
2101(chain B and (resid 6 through 7 or resid 9...B5 - 384
311(chain C and (resid 6 through 7 or resid 9...C6 - 7
321(chain C and (resid 6 through 7 or resid 9...C9 - 11
331(chain C and (resid 6 through 7 or resid 9...C0
341(chain C and (resid 6 through 7 or resid 9...C5 - 384
351(chain C and (resid 6 through 7 or resid 9...C39 - 46
361(chain C and (resid 6 through 7 or resid 9...C48 - 0
371(chain C and (resid 6 through 7 or resid 9...C6
381(chain C and (resid 6 through 7 or resid 9...C5 - 384
391(chain C and (resid 6 through 7 or resid 9...C122 - 130
3101(chain C and (resid 6 through 7 or resid 9...C133 - 140
3111(chain C and (resid 6 through 7 or resid 9...C144 - 145
3121(chain C and (resid 6 through 7 or resid 9...C3 - 155
3131(chain C and (resid 6 through 7 or resid 9...C157 - 158
3141(chain C and (resid 6 through 7 or resid 9...C5 - 384
3151(chain C and (resid 6 through 7 or resid 9...C168 - 17
3161(chain C and (resid 6 through 7 or resid 9...C184 - 200
3171(chain C and (resid 6 through 7 or resid 9...C203 - 230
3181(chain C and (resid 6 through 7 or resid 9...C23
3191(chain C and (resid 6 through 7 or resid 9...C6
3201(chain C and (resid 6 through 7 or resid 9...C238 - 240
3211(chain C and (resid 6 through 7 or resid 9...C5 - 384
3221(chain C and (resid 6 through 7 or resid 9...C283 - 31
3231(chain C and (resid 6 through 7 or resid 9...C313 - 347
3241(chain C and (resid 6 through 7 or resid 9...C5 - 384
3251(chain C and (resid 6 through 7 or resid 9...C5 - 384
3261(chain C and (resid 6 through 7 or resid 9...C364 - 379
3271(chain C and (resid 6 through 7 or resid 9...C381 - 383
411(chain D and (resid 6 through 7 or resid 9...D6 - 7
421(chain D and (resid 6 through 7 or resid 9...D9 - 11
431(chain D and (resid 6 through 7 or resid 9...D13 - 17
441(chain D and (resid 6 through 7 or resid 9...D19 - 24
451(chain D and (resid 6 through 7 or resid 9...D3 - 384
461(chain D and (resid 6 through 7 or resid 9...D39
471(chain D and (resid 6 through 7 or resid 9...D0
481(chain D and (resid 6 through 7 or resid 9...D3 - 384
491(chain D and (resid 6 through 7 or resid 9...D3 - 384
4101(chain D and (resid 6 through 7 or resid 9...D3 - 384
511(chain E and (resid 6 through 7 or resid 9...E6 - 7
521(chain E and (resid 6 through 7 or resid 9...E9 - 11
531(chain E and (resid 6 through 7 or resid 9...E13 - 17
541(chain E and (resid 6 through 7 or resid 9...E26 - 37
551(chain E and (resid 6 through 7 or resid 9...E39
561(chain E and (resid 6 through 7 or resid 9...E40
571(chain E and (resid 6 through 7 or resid 9...E3 - 384
581(chain E and (resid 6 through 7 or resid 9...E3 - 384
591(chain E and (resid 6 through 7 or resid 9...E3 - 384
5101(chain E and (resid 6 through 7 or resid 9...E3 - 384
611(chain F and (resid 6 through 7 or resid 9...F6 - 7
621(chain F and (resid 6 through 7 or resid 9...F9 - 11
631(chain F and (resid 6 through 7 or resid 9...F0
641(chain F and (resid 6 through 7 or resid 9...F2
651(chain F and (resid 6 through 7 or resid 9...F26 - 37
661(chain F and (resid 6 through 7 or resid 9...F39
671(chain F and (resid 6 through 7 or resid 9...F40
681(chain F and (resid 6 through 7 or resid 9...F6 - 384
691(chain F and (resid 6 through 7 or resid 9...F6 - 384
6101(chain F and (resid 6 through 7 or resid 9...F6 - 384
6111(chain F and (resid 6 through 7 or resid 9...F6 - 384
711(chain G and (resid 6 through 7 or resid 9...G6 - 7
721(chain G and (resid 6 through 7 or resid 9...G9 - 11
731(chain G and (resid 6 through 7 or resid 9...G13 - 17
741(chain G and (resid 6 through 7 or resid 9...G39
751(chain G and (resid 6 through 7 or resid 9...G407
761(chain G and (resid 6 through 7 or resid 9...G6 - 384
771(chain G and (resid 6 through 7 or resid 9...G6 - 384
781(chain G and (resid 6 through 7 or resid 9...G6 - 384
791(chain G and (resid 6 through 7 or resid 9...G6 - 384
7101(chain G and (resid 6 through 7 or resid 9...G6 - 384
7111(chain G and (resid 6 through 7 or resid 9...G6 - 384
811(chain H and (resid 6 through 7 or resid 9...H6 - 7
821(chain H and (resid 6 through 7 or resid 9...H9 - 11
831(chain H and (resid 6 through 7 or resid 9...H13 - 17
841(chain H and (resid 6 through 7 or resid 9...H39
851(chain H and (resid 6 through 7 or resid 9...H407
861(chain H and (resid 6 through 7 or resid 9...H5 - 384
871(chain H and (resid 6 through 7 or resid 9...H5 - 384
881(chain H and (resid 6 through 7 or resid 9...H5 - 384
891(chain H and (resid 6 through 7 or resid 9...H5 - 384
8101(chain H and (resid 6 through 7 or resid 9...H5 - 384
8111(chain H and (resid 6 through 7 or resid 9...H5 - 384
112chain IE401
212chain LE402
312chain MH401

NCS ensembles :
ID
1
2

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Components

#1: Protein
Acyl-CoA dehydrogenase /


Mass: 42247.723 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Gene: Tfu_1647 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q47PD7, Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor
#2: Chemical ChemComp-875 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-azanyl-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate


Mass: 560.347 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H26N6O13P2
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M Bis-Tis pH 9.0, 30% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 43185 / % possible obs: 95.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 74.12 Å2 / CC1/2: 0.931 / Net I/σ(I): 8
Reflection shellResolution: 3.1→3.2 Å / Num. unique obs: 43185 / CC1/2: 0.931

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
PDB_EXTRACT3.27data extraction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pfd

3pfd


Resolution: 3.13→27.46 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 2009 4.67 %
Rwork0.2147 41016 -
obs0.2174 43025 92.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.15 Å2 / Biso mean: 69.1934 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.13→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23238 0 108 0 23346
Biso mean--77.91 --
Num. residues----3026
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7304X-RAY DIFFRACTION6.834TORSIONAL
12B7304X-RAY DIFFRACTION6.834TORSIONAL
13C7304X-RAY DIFFRACTION6.834TORSIONAL
14D7304X-RAY DIFFRACTION6.834TORSIONAL
15E7304X-RAY DIFFRACTION6.834TORSIONAL
16F7304X-RAY DIFFRACTION6.834TORSIONAL
17G7304X-RAY DIFFRACTION6.834TORSIONAL
18H7304X-RAY DIFFRACTION6.834TORSIONAL
21E9X-RAY DIFFRACTION6.834TORSIONAL
22E9X-RAY DIFFRACTION6.834TORSIONAL
23H9X-RAY DIFFRACTION6.834TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.13-3.210.3671230.32582336245974
3.21-3.290.3471450.29653069321496
3.29-3.390.38871460.32532990313695
3.39-3.50.33641460.29492983312995
3.5-3.620.33321450.28072986313194
3.62-3.770.29021450.24842963310894
3.77-3.940.3251500.25972842299291
3.94-4.150.28281470.21292767291487
4.15-4.410.24531370.20062945308292
4.41-4.740.24211500.19293075322598
4.74-5.220.23861450.19643080322597
5.22-5.970.28921520.20843059321197
5.97-7.490.2821300.18982969309993
7.49-27.460.17371480.13452952310093

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