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- PDB-6ksb: Crystal Structure of E447A M130G Acyl-CoA Dehydrogenase FadE5 mut... -

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Basic information

Entry
Database: PDB / ID: 6ksb
TitleCrystal Structure of E447A M130G Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C16CoA
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / FadE5
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
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / PALMITIC ACID / Acyl-CoA dehydrogenase / Broad-specificity linear acyl-CoA dehydrogenase FadE5
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.973 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)136,74110
Polymers132,9382
Non-polymers3,8038
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-71 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.622, 199.096, 73.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acyl-CoA dehydrogenase


Mass: 66469.062 Da / Num. of mol.: 2 / Mutation: E447A,M130G
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

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Non-polymers , 5 types, 674 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H32O2
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C21H36N7O16P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 0.8 M NaH2PO4/1.2 M K2HPO4, 0.1 M acetate (pH 4.5), 1 mM FAD and 1.2 mM C16CoA

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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 S 6M / Detector: PIXEL / Date: Dec 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 95062 / % possible obs: 93.5 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.048 / Rrim(I) all: 0.151 / Χ2: 0.935 / Net I/σ(I): 4.9 / Num. measured all: 847026
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-26.21.01944480.6330.4121.1060.82388.6
2-2.047.30.94545440.7320.3541.0130.8890.2
2.04-2.088.10.88346040.7730.3140.940.8492.3
2.08-2.128.60.77846390.8160.2690.8250.86392.2
2.12-2.1790.69446770.8550.2360.7350.84892.7
2.17-2.229.10.61146910.8890.2060.6470.93193.4
2.22-2.278.70.52647090.9080.1830.5580.9494
2.27-2.348.90.4847340.9240.1650.5090.91893.8
2.34-2.49.70.42447290.950.140.4480.90393.6
2.4-2.489.70.38247210.9530.1260.4031.04193.4
2.48-2.579.50.31847160.9620.1050.3350.98293.5
2.57-2.679.30.26247300.9740.0880.2770.98493.5
2.67-2.88.80.22746990.9760.0780.2410.98992.7
2.8-2.949.30.19247110.9840.0640.2031.00192.3
2.94-3.139.70.16647150.9830.0540.1751.04892.8
3.13-3.379.50.13547030.9910.0440.1421.13492.2
3.37-3.718.90.10847430.9920.0370.1151.05992.5
3.71-4.249.40.09149580.9940.030.0961.00595.9
4.24-5.358.80.08151510.9950.0270.0850.91599
5.35-509.40.05654400.9980.0190.060.5699.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.973→49.344 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.4
RfactorNum. reflection% reflection
Rfree0.199 4418 5.09 %
Rwork0.1644 --
obs0.1662 86812 85.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.67 Å2 / Biso mean: 31.0329 Å2 / Biso min: 14.33 Å2
Refinement stepCycle: final / Resolution: 1.973→49.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9318 0 442 667 10427
Biso mean--33.75 34.71 -
Num. residues----1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149762
X-RAY DIFFRACTIONf_angle_d1.18213233
X-RAY DIFFRACTIONf_dihedral_angle_d9.585693
X-RAY DIFFRACTIONf_chiral_restr0.0621451
X-RAY DIFFRACTIONf_plane_restr0.0091696
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9732-1.99560.2641740.2089129240
1.9956-2.01910.239740.1942161951
2.0191-2.04370.2563880.2076190859
2.0437-2.06960.23531200.2016210566
2.0696-2.09680.24941100.1978223470
2.0968-2.12550.24521210.1821238075
2.1255-2.15590.23091460.176250379
2.1559-2.18810.20821450.1796258481
2.1881-2.22230.23081490.1686267083
2.2223-2.25870.23141330.178273686
2.2587-2.29770.20621550.1737279388
2.2977-2.33940.1831380.1738290190
2.3394-2.38440.19821490.1656290190
2.3844-2.43310.21471550.1618288691
2.4331-2.4860.23881490.1598293391
2.486-2.54380.20581580.1546293591
2.5438-2.60740.18511490.1485295693
2.6074-2.67790.181660.1552297693
2.6779-2.75670.18761850.1579293892
2.7567-2.84570.19991900.1588295892
2.8457-2.94740.19911560.1537299193
2.9474-3.06540.18351500.1566300092
3.0654-3.20490.20451570.1543298393
3.2049-3.37380.18091780.1483297093
3.3738-3.58510.17971730.1524300793
3.5851-3.86180.18131810.149299993
3.8618-4.25030.14681520.1416316697
4.2503-4.86480.17621520.1498328099
4.8648-6.12740.23951770.18273331100
6.1274-49.3440.22881880.20813459100

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