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- PDB-6lq4: Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant fr... -

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Basic information

Entry
Database: PDB / ID: 6lq4
TitleCrystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C14CoA
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


: / long-chain acyl-CoA dehydrogenase / medium-chain acyl-CoA dehydrogenase / long-chain fatty acyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / short-chain fatty acyl-CoA dehydrogenase activity / fatty acid metabolic process / flavin adenine dinucleotide binding / plasma membrane
Similarity search - Function
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 and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / MYRISTIC ACID / Acyl-CoA dehydrogenase / Broad-specificity linear acyl-CoA dehydrogenase FadE5
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 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
DepositionJan 13, 2020Deposition 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
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6498
Polymers133,0862
Non-polymers3,5636
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-60 kcal/mol
Surface area38960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.972, 206.435, 74.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-864-

HOH

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Components

#1: Protein Acyl-CoA dehydrogenase


Mass: 66543.203 Da / Num. of mol.: 2 / Mutation: E447A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: fadE5, ERS451418_00380 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D6G5A8, UniProt: Q3L887*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-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O2
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 0.1 M Hepes sodium (pH 7.0), 2% v/v PEG 400, 2 M (NH4)2SO4, 1 mM FAD and 1.2 mM C18CoA

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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: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.4→19.647 Å / Num. obs: 59495 / % possible obs: 99.7 % / Redundancy: 13.382 % / Biso Wilson estimate: 27.214 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.205 / Rrim(I) all: 0.213 / Χ2: 0.968 / Net I/σ(I): 12.65 / Num. measured all: 796163 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.4613.3410.7313.8858179436243610.9250.76100
2.46-2.5312.8340.6274.4853915420342010.9360.653100
2.53-2.612.6450.5595.0151973411741100.9370.58399.8
2.6-2.6813.9760.5415.6156128401640160.960.562100
2.68-2.7713.9690.476.3854312388838880.9670.488100
2.77-2.8713.8610.4077.1752546379137910.9710.423100
2.87-2.9813.8310.3638.1250194362936290.9750.377100
2.98-3.113.6610.3039.4948058351835180.9830.314100
3.1-3.2413.2050.25111.0844792339233920.9880.261100
3.24-3.3912.3460.18813.6139607321332080.990.19699.8
3.39-3.5814.1710.1716.2143321305730570.9950.176100
3.58-3.7914.0030.13619.5441114293729360.9960.141100
3.79-4.0613.8250.11222.8838156276027600.9970.116100
4.06-4.3813.5350.10223.7934906257925790.9970.106100
4.38-4.812.5070.09524.5629417235323520.9970.099100
4.8-5.3712.8790.10422.927985217321730.9970.108100
5.37-6.213.6640.12919.7726427193519340.9960.13499.9
6.2-7.5913.2290.1122.1821736164516430.9970.11499.9
7.59-10.7311.6540.05931.8715127129812980.9990.062100
10.73-19.64712.7430.05834.9582707946490.9990.06181.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→19.647 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 2.3 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 2708 4.99 %
Rwork0.1613 51565 -
obs0.1634 54273 91.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.1 Å2 / Biso mean: 25.934 Å2 / Biso min: 12.99 Å2
Refinement stepCycle: final / Resolution: 2.4→19.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9289 0 392 677 10358
Biso mean--27.04 28.25 -
Num. residues----1214
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.44360.24121330.2044277795
2.4436-2.49050.23661550.1934276494
2.4905-2.54120.22541410.1865276994
2.5412-2.59630.24811480.187273894
2.5963-2.65660.23451450.1855278694
2.6566-2.72290.23441440.1839276694
2.7229-2.79630.21691250.1732275494
2.7963-2.87830.21331310.1756276994
2.8783-2.97090.24951490.1776276493
2.9709-3.07670.22631410.1757271993
3.0767-3.19940.23761440.1719275193
3.1994-3.34440.19581630.1613271692
3.3444-3.51970.21281390.1602273091
3.5197-3.73880.18281570.1525268491
3.7388-4.02520.17451380.1318268190
4.0252-4.42610.1591400.1235265889
4.4261-5.0570.15771370.1258265388
5.057-6.33560.20971400.1725261385
6.3356-19.6470.18971380.1672247378

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