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- PDB-6kse: Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant fr... -

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Basic information

Entry
Database: PDB / ID: 6kse
TitleCrystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria tuberculosisin complex with C18CoA
ComponentsAcyl-CoA dehydrogenase FadE5
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


short-chain acyl-CoA dehydrogenase / : / oxidoreductase activity, acting on the CH-CH group of donors / response to host immune response / flavin adenine dinucleotide binding / extracellular region / plasma membrane
Similarity search - Function
Broad-specificity linear acyl-CoA dehydrogenase FadE5-like / Acyl-CoA dehydrogenase, N-terminal, bacteria / Acyl-CoA dehydrogenase N terminal / Acetyl-CoA dehydrogenase-like C-terminal domain / Acetyl-CoA dehydrogenase C-terminal like / Acyl-CoA dehydrogenase/oxidase C-terminal / 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 ...Broad-specificity linear acyl-CoA dehydrogenase FadE5-like / Acyl-CoA dehydrogenase, N-terminal, bacteria / Acyl-CoA dehydrogenase N terminal / Acetyl-CoA dehydrogenase-like C-terminal domain / Acetyl-CoA dehydrogenase C-terminal like / Acyl-CoA dehydrogenase/oxidase C-terminal / 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 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / STEAROYL-COENZYME A / Acyl-CoA dehydrogenase FadE5 / Probable acyl-CoA dehydrogenase FadE5
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsLiu, X. / Chen, X.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria.
Authors: Chen, X. / Chen, J. / Yan, B. / Zhang, W. / Guddat, L.W. / Liu, X. / Rao, Z.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Acyl-CoA dehydrogenase FadE5
B: Acyl-CoA dehydrogenase FadE5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7576
Polymers132,1182
Non-polymers3,6394
Water17,799988
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-73 kcal/mol
Surface area38580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.451, 147.597, 66.224
Angle α, β, γ (deg.)90.000, 93.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acyl-CoA dehydrogenase FadE5 / Putative acyl-CoA dehydrogenase FadE5


Mass: 66058.953 Da / Num. of mol.: 2 / Mutation: E447A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fadE5 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A045J1P5, UniProt: O53666*PLUS, short-chain acyl-CoA dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ST9 / STEAROYL-COENZYME A


Mass: 1033.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H70N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.68 % / Mosaicity: 0.892 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5 / Details: 20% (w/v) PEG 3350 and 2 M potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. obs: 79391 / % possible obs: 98.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.056 / Rrim(I) all: 0.135 / Χ2: 0.922 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.80.58532710.7720.3150.6690.80981.6
2.03-2.0740.53236050.8310.2790.6050.83488.9
2.07-2.114.40.55738260.8090.2870.630.99395.1
2.11-2.154.80.51139730.8650.2530.5720.83498.4
2.15-2.25.10.47539890.8990.2280.5290.85299.3
2.2-2.255.30.46840310.8960.2210.5191.08100
2.25-2.315.50.48340400.9320.2260.5350.919100
2.31-2.375.60.36240070.9460.1670.40.88199.9
2.37-2.445.60.3240350.9520.1490.3540.886100
2.44-2.525.60.28440400.9540.1310.3130.928100
2.52-2.6160.24440910.9720.1080.2680.936100
2.61-2.716.30.21939990.9790.0960.240.931100
2.71-2.846.20.18740620.9810.0820.2040.95100
2.84-2.996.20.15340300.9860.0670.1670.973100
2.99-3.175.90.12540450.9880.0560.1370.992100
3.17-3.425.90.09940220.9910.0440.1091.04100
3.42-3.766.40.08840640.9940.0380.0961.079100
3.76-4.316.20.06640510.9960.0290.0720.885100
4.31-5.435.90.05840710.9970.0260.0630.795100
5.43-506.10.05241390.9970.0230.0570.736100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.998→49.249 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.99
RfactorNum. reflection% reflection
Rfree0.2001 3456 4.87 %
Rwork0.1664 --
obs0.168 70968 87.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.41 Å2 / Biso mean: 30.7452 Å2 / Biso min: 12.51 Å2
Refinement stepCycle: final / Resolution: 1.998→49.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9254 0 434 992 10680
Biso mean--35.79 33.71 -
Num. residues----1214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059693
X-RAY DIFFRACTIONf_angle_d0.68513154
X-RAY DIFFRACTIONf_dihedral_angle_d6.7575636
X-RAY DIFFRACTIONf_chiral_restr0.0421464
X-RAY DIFFRACTIONf_plane_restr0.0031672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.998-2.02490.2651630.2236128342
2.0249-2.05380.2682700.2087149549
2.0538-2.08450.2066730.1957170455
2.0845-2.11710.29621050.2075194564
2.1171-2.15180.2125980.2103221271
2.1518-2.18890.23391510.2022228777
2.1889-2.22870.26961320.2088242678
2.2287-2.27160.31341030.2406253782
2.2716-2.31790.22261370.1962269788
2.3179-2.36830.21311240.1847287994
2.3683-2.42340.23121640.194295796
2.4234-2.4840.21641760.1831301398
2.484-2.55120.2581650.17693041100
2.5512-2.62620.19992000.17093041100
2.6262-2.7110.21511470.1783093100
2.711-2.80790.22021580.1743062100
2.8079-2.92030.21341360.17163092100
2.9203-3.05320.21641470.17063083100
3.0532-3.21410.22041840.17153054100
3.2141-3.41550.18111500.15883091100
3.4155-3.67910.19961600.15823124100
3.6791-4.04920.17941540.13833061100
4.0492-4.63470.12971660.12573072100
4.6347-5.83780.16641420.14153120100
5.8378-49.2490.18221510.1643143100

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