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

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Basic information

Entry
Database: PDB / ID: 6lpy
TitleCrystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C4CoA
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 / : / 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
butanoic acid / COENZYME A / 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: 1.9 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)136,3698
Polymers133,0862
Non-polymers3,2826
Water21,9781220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-57 kcal/mol
Surface area38840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.077, 206.705, 74.129
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-1045-

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-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H8O2
#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.: 1220 / 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: 2.82 Å3/Da / Density % sol: 56.43 %
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: 1.9→19.671 Å / Num. obs: 119265 / % possible obs: 99.9 % / Redundancy: 13.392 % / Biso Wilson estimate: 27.868 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.135 / Χ2: 0.986 / Net I/σ(I): 16.59 / Num. measured all: 1597162 / Scaling rejects: 89
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
1.9-1.9513.8340.9912.85120947874587430.8571.029100
1.95-213.6670.7973.55116143849884980.90.828100
2-2.0613.4650.6164.57111287826682650.9350.641100
2.06-2.1213.170.4995.58106294807180710.9480.519100
2.12-2.1912.4150.46.7596667778677860.9660.417100
2.19-2.2713.7140.3278.66103557755175510.980.34100
2.27-2.3613.8790.2849.94101563731973180.9840.295100
2.36-2.4513.7920.24211.3897150704670440.9880.252100
2.45-2.5613.6810.19813.6692631677167710.9930.206100
2.56-2.6913.4320.16615.8786424643464340.9940.172100
2.69-2.8312.340.14317.2776149617161710.9950.149100
2.83-313.860.12321.0481232586158610.9960.128100
3-3.2113.9560.125.5776561548654860.9980.104100
3.21-3.4713.6360.07831.4769964513151310.9980.081100
3.47-3.813.2170.06436.6462846475547550.9990.067100
3.8-4.2511.9820.05340.3251677431443130.9990.055100
4.25-4.9113.8740.04846.2353402384938490.9990.05100
4.91-6.0113.470.05241.2243764324932490.9990.055100
6.01-8.511.9320.04741.5630891259125890.9990.04999.9
8.5-19.67113.0530.03455.5418013152613800.9990.03590.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→19.671 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2.11 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 5596 4.96 %
Rwork0.1567 107317 -
obs0.1589 112913 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.78 Å2 / Biso mean: 26.2256 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 1.9→19.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9289 0 212 1220 10721
Biso mean--37.05 35.75 -
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 (%)
1.9-1.92160.30771960.2415367398
1.9216-1.94420.26871790.2304366298
1.9442-1.96790.27322070.2277362798
1.9679-1.99270.32661710.2255372299
1.9927-2.01890.28341700.2078370798
2.0189-2.04660.26611840.1982367898
2.0466-2.07580.2022150.1757362098
2.0758-2.10670.23212010.1741363098
2.1067-2.13960.2551930.1733366097
2.1396-2.17460.22151980.1711363697
2.1746-2.21210.22261780.1677362297
2.2121-2.25230.20651940.1661363297
2.2523-2.29550.21491810.1598361996
2.2955-2.34230.22361960.1576357696
2.3423-2.39310.20622020.1526361296
2.3931-2.44870.23081810.1541356396
2.4487-2.50980.20981800.1548362896
2.5098-2.57750.20421750.1495358795
2.5775-2.65320.1981690.1455360595
2.6532-2.73860.20381960.1474355395
2.7386-2.83620.21461730.1487356895
2.8362-2.94940.18331930.1523353394
2.9494-3.08320.19241970.1583356094
3.0832-3.24510.19121660.1568354893
3.2451-3.44740.19431760.1518349893
3.4474-3.71190.18551810.1453353892
3.7119-4.08240.15851740.1286348191
4.0824-4.66630.15652010.125342289
4.6663-5.85320.18161950.1519334787
5.8532-19.6710.17311740.1583321079

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