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- PDB-6ks9: Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant fr... -

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Basic information

Entry
Database: PDB / ID: 6ks9
TitleCrystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis
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
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase / Broad-specificity linear acyl-CoA dehydrogenase FadE5
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,33011
Polymers133,0862
Non-polymers2,2449
Water15,313850
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12550 Å2
ΔGint-134 kcal/mol
Surface area39370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.692, 205.245, 73.936
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-1257-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / 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: 2.78 Å3/Da / Density % sol: 55.83 % / Mosaicity: 0.375 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 0.1 M Hepes sodium (pH 7.0), 2% v/v PEG 400, and 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 100685 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.041 / Rrim(I) all: 0.138 / Χ2: 0.987 / Net I/σ(I): 5 / Num. measured all: 1119738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0310.50.82849950.8020.2670.870.938100
2.03-2.0710.10.72849530.8360.240.7670.957100
2.07-2.1111.60.64649940.8810.1970.6760.973100
2.11-2.1511.60.56549420.9130.1730.5910.984100
2.15-2.211.60.47449720.9340.1450.4960.99100
2.2-2.2511.40.47649740.9410.1480.4991.285100
2.25-2.3111.30.3749980.960.1150.3880.997100
2.31-2.3711.10.3349930.9660.1030.3471.015100
2.37-2.4410.90.30849970.970.0970.3230.992100
2.44-2.52100.24949650.9780.0820.2621.022100
2.52-2.6111.70.22250200.9840.0680.2321.034100
2.61-2.7111.60.19750000.9870.060.2061.033100
2.71-2.8411.50.17250460.990.0530.181.019100
2.84-2.9911.40.14550150.9920.0450.1521.001100
2.99-3.1710.90.11850230.9940.0370.1241.00999.9
3.17-3.4210.80.09150510.9960.0280.0951.039100
3.42-3.7611.70.07550810.9970.0230.0790.986100
3.76-4.3111.40.06151120.9980.0190.0640.927100
4.31-5.4310.60.05551630.9980.0180.0580.805100
5.43-5010.70.04953910.9990.0150.0510.72199.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→48.846 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 4986 4.96 %
Rwork0.1678 95585 -
obs0.1688 100571 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 291.32 Å2 / Biso mean: 32.9375 Å2 / Biso min: 13.18 Å2
Refinement stepCycle: final / Resolution: 2.001→48.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9271 0 202 850 10323
Biso mean--62.26 36.57 -
Num. residues----1211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039628
X-RAY DIFFRACTIONf_angle_d0.60613056
X-RAY DIFFRACTIONf_dihedral_angle_d8.5676685
X-RAY DIFFRACTIONf_chiral_restr0.0381441
X-RAY DIFFRACTIONf_plane_restr0.0041682
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0012-2.02390.24441650.2032279089
2.0239-2.04780.25211690.20523157100
2.0478-2.07270.23661800.20473129100
2.0727-2.0990.23251440.19493165100
2.099-2.12660.21431690.18583176100
2.1266-2.15570.20081520.18183175100
2.1557-2.18650.21051680.18073176100
2.1865-2.21920.2491490.17913162100
2.2192-2.25380.21821640.18243151100
2.2538-2.29080.17911600.16923168100
2.2908-2.33030.1811450.16863203100
2.3303-2.37270.19351760.17113149100
2.3727-2.41830.18291680.16893168100
2.4183-2.46770.2051590.1673210100
2.4677-2.52130.16291580.16243170100
2.5213-2.580.21861600.16323175100
2.58-2.64450.18451670.16013215100
2.6445-2.7160.18531820.16243150100
2.716-2.79590.1731640.16213186100
2.7959-2.88610.18191460.16423202100
2.8861-2.98920.17151840.16173214100
2.9892-3.10890.19641630.16643185100
3.1089-3.25040.18171470.16993217100
3.2504-3.42170.19011780.16713208100
3.4217-3.6360.20161710.16413209100
3.636-3.91660.17731810.14653235100
3.9166-4.31060.15961830.14083229100
4.3106-4.93380.14561890.13613259100
4.9338-6.21410.19251610.18853315100
6.2141-48.8460.21311840.20593437100

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