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- PDB-6lq1: Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant fr... -

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Basic information

Entry
Database: PDB / ID: 6lq1
TitleCrystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C8CoA
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


long-chain acyl-CoA dehydrogenase / long-chain fatty acyl-CoA dehydrogenase activity / medium-chain acyl-CoA dehydrogenase / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / medium-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 / FLAVIN-ADENINE DINUCLEOTIDE / OCTANOIC ACID (CAPRYLIC 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: 2.8 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)136,4818
Polymers133,0862
Non-polymers3,3956
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15080 Å2
ΔGint-57 kcal/mol
Surface area39280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.295, 206.431, 74.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 / 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-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H16O2
#4: Chemical ChemComp-COA / COENZYME A / 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 / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
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: 2.8→19.668 Å / Num. obs: 37912 / % possible obs: 99.6 % / Redundancy: 13.02 % / Biso Wilson estimate: 18.818 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.207 / Χ2: 0.947 / Net I/σ(I): 16.27 / Num. measured all: 493628
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
2.8-2.8711.9590.4956.0933078276727660.9550.518100
2.87-2.9512.3590.4556.8133195268626860.9640.475100
2.95-3.0413.3820.4187.8535194263026300.9740.434100
3.04-3.1313.2010.3668.9833834256325630.980.381100
3.13-3.2313.230.31810.5732719247324730.9860.331100
3.23-3.3513.3740.27112.6931910238723860.990.282100
3.35-3.4713.4580.25514.231196231823180.9920.266100
3.47-3.6113.3060.23115.9329819224122410.9940.24100
3.61-3.7812.1060.1917.6325980214621460.9940.198100
3.78-3.9613.3640.16321.2827677207120710.9950.169100
3.96-4.1713.9050.14722.8527073194719470.9970.153100
4.17-4.4313.7610.13423.9925747187118710.9980.14100
4.43-4.7313.550.12425.2523902176417640.9970.129100
4.73-5.1113.1880.12624.4221576163916360.9970.13199.8
5.11-5.611.8280.14919.9817908151415140.9960.155100
5.6-6.2613.3110.15719.918516139213910.9960.16399.9
6.26-7.2313.5160.13322.3416706123612360.9970.138100
7.23-8.8512.8040.08529.5413547105810580.9980.088100
8.85-12.5211.1850.06433.4994968508490.9980.06899.9
12.52-19.66812.4450.07233.1445555113660.9980.07571.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→19.668 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.86 / Phase error: 23.03
RfactorNum. reflection% reflection
Rfree0.2261 1688 4.93 %
Rwork0.1759 --
obs0.1784 34239 90.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.79 Å2 / Biso mean: 22.2655 Å2 / Biso min: 7.6 Å2
Refinement stepCycle: final / Resolution: 2.8→19.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9289 0 352 254 9895
Biso mean--20.93 18.1 -
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 (%)
2.8-2.88220.31041600.2375277995
2.8822-2.97490.30321540.2267280795
2.9749-3.08080.28281340.2314277094
3.0808-3.20370.33011220.2184280794
3.2037-3.34880.2511410.196277694
3.3488-3.52440.23821440.1924277193
3.5244-3.74380.24091330.168275092
3.7438-4.03060.21221310.1475269890
4.0306-4.4320.15691420.1345265589
4.432-5.06370.161540.1316264288
5.0637-6.3440.20271450.1712261085
6.344-19.6680.19661280.1608248678

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