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- PDB-7xly: Crystal structure of FadA2 (Rv0243) from the fatty acid metabolic... -

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Basic information

Entry
Database: PDB / ID: 7xly
TitleCrystal structure of FadA2 (Rv0243) from the fatty acid metabolic pathway of Mycobacterium tuberculosis
ComponentsProbable acetyl-CoA acyltransferase FadA2 (3-ketoacyl-CoA thiolase) (Beta-ketothiolase)
KeywordsTRANSFERASE / acetyl-CoA acetyltransferase / Fatty acid metabolism / Mycobacterium tuberculosis
Function / homology
Function and homology information


biological process involved in interaction with host / acyltransferase activity, transferring groups other than amino-acyl groups / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
: / Thiolase, active site / Thiolases active site. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
Probable acetyl-CoA acyltransferase FadA2 (3-ketoacyl-CoA thiolase) (Beta-ketothiolase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSingh, R. / Kundu, P. / Singh, B.K. / Bhattacharyya, S. / Das, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR12404/BRB/10/1362/2014 India
CitationJournal: Febs J. / Year: 2023
Title: Crystal structure of FadA2 thiolase from Mycobacterium tuberculosis and prediction of its substrate specificity and membrane-anchoring properties.
Authors: Singh, R. / Kundu, P. / Mishra, V.K. / Singh, B.K. / Bhattacharyya, S. / Das, A.K.
History
DepositionApr 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Probable acetyl-CoA acyltransferase FadA2 (3-ketoacyl-CoA thiolase) (Beta-ketothiolase)
A: Probable acetyl-CoA acyltransferase FadA2 (3-ketoacyl-CoA thiolase) (Beta-ketothiolase)
B: Probable acetyl-CoA acyltransferase FadA2 (3-ketoacyl-CoA thiolase) (Beta-ketothiolase)
D: Probable acetyl-CoA acyltransferase FadA2 (3-ketoacyl-CoA thiolase) (Beta-ketothiolase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,7975
Polymers184,7004
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-18 kcal/mol
Surface area51170 Å2
Unit cell
Length a, b, c (Å)109.782, 109.782, 353.112
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Probable acetyl-CoA acyltransferase FadA2 (3-ketoacyl-CoA thiolase) (Beta-ketothiolase)


Mass: 46175.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: fadA2, Rv0243 / Production host: Escherichia coli (E. coli) / References: UniProt: O86361, acetyl-CoA C-acetyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl, 1.5M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.9→47.54 Å / Num. obs: 55758 / % possible obs: 99.21 % / Redundancy: 2 % / Biso Wilson estimate: 75.03 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.049 / Net I/σ(I): 13.92
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 1.01 / Num. unique obs: 5442 / CC1/2: 0.932 / Rpim(I) all: 0.35 / % possible all: 98.97

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DV2

6dv2


Resolution: 2.9→47.54 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 2687 4.85 %
Rwork0.2455 52722 -
obs0.2475 55409 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.94 Å2 / Biso mean: 99.1511 Å2 / Biso min: 53.21 Å2
Refinement stepCycle: final / Resolution: 2.9→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11271 0 5 0 11276
Biso mean--134.56 --
Num. residues----1585
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.950.46691190.43472743286299
2.95-3.010.38931620.38752691285399
3.01-3.070.51071440.36812686283098
3.07-3.140.37151320.34592718285098
3.14-3.210.36671410.33112699284099
3.21-3.290.40631140.32182753286799
3.29-3.380.33461260.3012747287399
3.38-3.480.331310.31022732286399
3.48-3.590.34211410.28372741288299
3.59-3.720.32361380.25952742288099
3.72-3.870.30281340.26412763289799
3.87-4.040.30391310.243428102941100
4.05-4.260.28471560.222927352891100
4.26-4.520.25461710.204627852956100
4.53-4.870.21591490.193828002949100
4.87-5.360.20771480.207428172965100
5.36-6.140.23661630.228928312994100
6.14-7.720.27681160.236129053021100
7.73-47.540.26191710.205530243195100

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