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

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Basic information

Entry
Database: PDB / ID: 6kri
TitleCrystal Structure of Acyl-CoA Dehydrogenase FadE5 from Mycobacteria smegmatis with product released
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
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: 1.604 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 21, 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)134,9666
Polymers133,2022
Non-polymers1,7634
Water24,8971382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-88 kcal/mol
Surface area39520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.934, 205.903, 73.951
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-1223-

HOH

21B-1461-

HOH

31B-1483-

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 / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1382 / 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: 56.05 % / Mosaicity: 0.377 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5 / Details: 2M (NH4)2SO4, 2% (v/V) PEG400, 0.1M Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 194416 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.054 / Rrim(I) all: 0.14 / Χ2: 0.966 / Net I/σ(I): 5 / Num. measured all: 1263335
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.635.81.28996480.450.5871.4190.9100
1.63-1.666.21.15196660.560.51.2570.918100
1.66-1.696.41.02496210.6340.4341.1140.919100
1.69-1.726.50.90897040.6960.3810.9860.93299.9
1.72-1.766.40.77695890.7490.3290.8450.93999.6
1.76-1.86.10.63895510.7850.2790.6980.96998.3
1.8-1.856.50.53795340.8560.2260.5840.99498.6
1.85-1.96.80.45696880.9020.1880.4941.016100
1.9-1.956.80.3896710.9310.1570.4120.9999.9
1.95-2.026.70.30996740.9520.1280.3350.998100
2.02-2.096.50.25197450.9620.1060.2731.01599.9
2.09-2.176.10.20695760.9670.090.2261.04598.3
2.17-2.276.70.17996670.9770.0740.1941.14799.4
2.27-2.396.80.15297590.9840.0630.1651.019100
2.39-2.546.80.13497640.9850.0550.1461.013100
2.54-2.746.60.11897750.9860.050.1280.99699.9
2.74-3.016.50.10597280.9880.0440.1140.97199.2
3.01-3.456.90.09298750.9910.0380.10.96599.9
3.45-4.346.40.08199110.990.0350.0880.93299.5
4.34-506.60.065102700.9940.0270.070.64599.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.604→44.748 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.55
RfactorNum. reflection% reflection
Rfree0.1908 9218 4.94 %
Rwork0.1666 --
obs0.1678 186737 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 279.73 Å2 / Biso mean: 21.5687 Å2 / Biso min: 6.51 Å2
Refinement stepCycle: final / Resolution: 1.604→44.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9277 0 177 1387 10841
Biso mean--33.4 31.42 -
Num. residues----1210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089603
X-RAY DIFFRACTIONf_angle_d0.88313022
X-RAY DIFFRACTIONf_dihedral_angle_d7.4317750
X-RAY DIFFRACTIONf_chiral_restr0.051439
X-RAY DIFFRACTIONf_plane_restr0.0061682
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.604-1.62220.27971480.2724275545
1.6222-1.64130.27181920.2644398164
1.6413-1.66130.29082400.2602514783
1.6613-1.68240.27742860.2424569093
1.6824-1.70450.27193050.2329591097
1.7045-1.72790.24913230.224599398
1.7279-1.75250.26273130.2193605998
1.7525-1.77870.2493190.2147606698
1.7787-1.80650.23592950.2088592096
1.8065-1.83610.22083090.1978594497
1.8361-1.86780.20253180.18436147100
1.8678-1.90170.20433020.18256183100
1.9017-1.93830.20523290.17326120100
1.9383-1.97790.20363250.16986144100
1.9779-2.02090.19453400.1656153100
2.0209-2.06790.18383150.15846162100
2.0679-2.11960.18733180.15596195100
2.1196-2.17690.18383050.1489605598
2.1769-2.2410.17122980.1483616899
2.241-2.31330.173370.14266145100
2.3133-2.3960.18213100.14226202100
2.396-2.49190.18083040.14376196100
2.4919-2.60530.17733410.14166201100
2.6053-2.74260.18223190.14676216100
2.7426-2.91440.17063130.1532616999
2.9144-3.13940.17643550.16066200100
3.1394-3.45520.18363210.15736271100
3.4552-3.9550.1723410.14926315100
3.955-4.98180.15463430.1433629699
4.9818-44.7480.21033540.2054651699

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