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- PDB-6kpt: Crystal Structure of Acyl-CoA Dehydrogenase FadE5 from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 6kpt
TitleCrystal Structure of Acyl-CoA Dehydrogenase FadE5 from Mycobacteria smegmatis
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Tuberculosis / beta-oxidation / ANTIBIOTIC
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 / SAD / Resolution: 1.963 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 16, 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

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,7744
Polymers133,2022
Non-polymers1,5712
Water18,9341051
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-68 kcal/mol
Surface area39550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.202, 97.825, 205.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-1211-

HOH

21B-1315-

HOH

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Components

#1: Protein Acyl-CoA dehydrogenase


Mass: 66601.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: fadE5, ERS451418_00380 / Production host: Escherichia coli (E. coli)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1051 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 2M (NH4)2 SO4, 2%(v/v) PEG400, 0.1 M Acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9748 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9748 Å / Relative weight: 1
ReflectionResolution: 1.94→40 Å / Num. obs: 106041 / % possible obs: 100 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.05 / Rrim(I) all: 0.118 / Χ2: 0.824 / Net I/σ(I): 7.8 / Num. measured all: 571513
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.974.90.41252200.8960.2040.4610.81999.9
1.97-2.015.40.34752030.9320.1630.3850.845100
2.01-2.055.60.32452680.9270.1520.3590.863100
2.05-2.095.50.29252270.9370.1370.3240.902100
2.09-2.145.50.25752460.9490.1210.2850.904100
2.14-2.185.30.22652600.9560.1080.2510.913100
2.18-2.245.30.20652270.9550.0990.2290.95100
2.24-2.35.40.19452640.9660.0920.2150.97899.9
2.3-2.375.40.17152790.9730.080.1890.94100
2.37-2.445.60.15652720.9760.0720.1720.916100
2.44-2.535.50.13952690.9780.0650.1540.911100
2.53-2.635.30.12552570.9820.0590.1380.884100
2.63-2.755.30.11452850.9830.0540.1260.854100
2.75-2.95.30.10652830.9860.050.1170.854100
2.9-3.085.60.09553420.9870.0440.1050.802100
3.08-3.325.50.08453210.990.0390.0930.793100
3.32-3.655.30.07353610.9910.0350.0810.716100
3.65-4.185.40.06753580.9930.0310.0740.653100
4.18-5.265.30.0654380.9930.0280.0660.55499.9
5.26-405.20.05456610.9950.0260.060.44799.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.963→39.793 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 5240 4.96 %
Rwork0.1512 100435 -
obs0.1532 105675 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.43 Å2 / Biso mean: 26.099 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.963→39.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9333 0 167 1055 10555
Biso mean--20.41 31.08 -
Num. residues----1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0169651
X-RAY DIFFRACTIONf_angle_d1.39813084
X-RAY DIFFRACTIONf_dihedral_angle_d7.3237805
X-RAY DIFFRACTIONf_chiral_restr0.0691446
X-RAY DIFFRACTIONf_plane_restr0.011694
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.963-1.98520.23921210.1979192558
1.9852-2.00860.24111620.1744336699
2.0086-2.03310.19351820.1663316100
2.0331-2.05880.20451710.15863348100
2.0588-2.08590.19511740.15983381100
2.0859-2.11450.19511640.1533337499
2.1145-2.14470.19741850.15633304100
2.1447-2.17670.20541720.1523338699
2.1767-2.21070.19291560.1489333499
2.2107-2.24690.20361680.1467333299
2.2469-2.28570.18181920.14763335100
2.2857-2.32720.18891470.14843449100
2.3272-2.3720.21191700.14843356100
2.372-2.42040.20181580.14483387100
2.4204-2.4730.19221750.14733398100
2.473-2.53050.18721730.14563367100
2.5305-2.59380.21591820.14733359100
2.5938-2.66390.21241890.14383408100
2.6639-2.74230.19451890.14823385100
2.7423-2.83080.18541620.14513390100
2.8308-2.93190.19412110.15633370100
2.9319-3.04930.19841600.15863417100
3.0493-3.1880.21081770.15973411100
3.188-3.3560.20211760.15453421100
3.356-3.56610.21911930.1533418100
3.5661-3.84130.16461780.14543433100
3.8413-4.22740.16651740.12663465100
4.2274-4.83820.1382200.123422100
4.8382-6.09220.18621810.15843521100
6.0922-39.7930.19041780.1931365799

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