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- PDB-6lq3: Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant fr... -

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Basic information

Entry
Database: PDB / ID: 6lq3
TitleCrystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C12CoA
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


long-chain acyl-CoA dehydrogenase / : / medium-chain acyl-CoA dehydrogenase / short-chain acyl-CoA dehydrogenase / long-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acyl-CoA dehydrogenase activity / short-chain fatty acyl-CoA dehydrogenase activity / fatty acid metabolic process / flavin adenine dinucleotide binding
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 / LAURIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase / Broad-specificity linear acyl-CoA dehydrogenase FadE5
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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 12, 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)136,5938
Polymers133,0862
Non-polymers3,5076
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15290 Å2
ΔGint-57 kcal/mol
Surface area39130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.009, 206.376, 73.953
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-936-

HOH

21B-1018-

HOH

31B-1020-

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-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H24O2
#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.: 448 / 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: 56.23 %
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: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→19.946 Å / Num. obs: 52711 / % possible obs: 99.7 % / Redundancy: 13.346 % / Biso Wilson estimate: 30.329 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.168 / Χ2: 0.947 / Net I/σ(I): 15.49 / Num. measured all: 703464 / Scaling rejects: 13
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
2.5-2.5613.7510.5954.7453064386038590.9430.617100
2.56-2.6413.5750.5295.3250879374837480.9480.55100
2.64-2.7113.2560.475.8848078362736270.9590.488100
2.71-2.812.2510.4096.3543735357035700.9640.427100
2.8-2.8913.0130.3687.2645025346034600.9730.383100
2.89-2.9914.2550.3288.5947328332033200.980.34100
2.99-3.114.1070.2879.845411322032190.9840.297100
3.1-3.2314.0250.23511.7543829312531250.990.244100
3.23-3.3713.8440.1814.941435299329930.9940.187100
3.37-3.5413.6870.15616.9239186286328630.9950.162100
3.54-3.7313.4410.12720.3536451271227120.9970.132100
3.73-3.9512.6040.10323.4432570258425840.9970.107100
3.95-4.2311.760.08725.1728671243924380.9980.091100
4.23-4.5613.9230.0829.7331648227322730.9980.083100
4.56-513.7670.07630.7728925210121010.9980.079100
5-5.5913.6090.08926.3926184192419240.9980.093100
5.59-6.4513.0120.123.8622199170617060.9970.104100
6.45-7.9111.760.07328.8717134145814570.9990.07699.9
7.91-11.1812.6150.0444.5114759117011700.9990.042100
11.18-19.94612.3720.04443.7469537055620.9990.04679.7

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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: 2.5→19.946 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2.4 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 2411 5.02 %
Rwork0.1668 45620 -
obs0.169 48031 91.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.65 Å2 / Biso mean: 28.5666 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 2.5→19.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9289 0 376 448 10113
Biso mean--37.61 29.51 -
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 (%)
2.5-2.55090.25161570.1886274794
2.5509-2.60630.27291350.1837272195
2.6063-2.66680.2481430.1776275895
2.6668-2.73330.21051470.1739275994
2.7333-2.8070.24291240.1721273395
2.807-2.88940.20021300.1778275294
2.8894-2.98230.24371670.1819270094
2.9823-3.08860.23741370.1818273993
3.0886-3.21170.24991430.1787270293
3.2117-3.35730.24061370.1717271392
3.3573-3.53330.20851530.1683269792
3.5333-3.75330.21071410.1626266891
3.7533-4.04090.20091570.1469265291
4.0409-4.44350.17191310.1409265989
4.4435-5.07720.1551390.1434260688
5.0772-6.36210.21221380.1857257085
6.3621-19.9460.17771320.1704244478

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