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- PDB-5du6: Crystal structure of M. tuberculosis EchA6 bound to ligand GSK059A. -

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Basic information

Entry
Database: PDB / ID: 5du6
TitleCrystal structure of M. tuberculosis EchA6 bound to ligand GSK059A.
ComponentsProbable enoyl-CoA hydratase echA6
KeywordsLYASE / enoyl-CoA hydratase-like
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / peptidoglycan-based cell wall / plasma membrane
Similarity search - Function
Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-G59 / Probable enoyl-CoA hydratase EchA6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsCox, J.A.G. / Besra, G.S. / Futterer, K.
CitationJournal: Nat Microbiol / Year: 2016
Title: THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria.
Authors: Cox, J.A. / Abrahams, K.A. / Alemparte, C. / Ghidelli-Disse, S. / Rullas, J. / Angulo-Barturen, I. / Singh, A. / Gurcha, S.S. / Nataraj, V. / Bethell, S. / Remuinan, M.J. / Encinas, L. / ...Authors: Cox, J.A. / Abrahams, K.A. / Alemparte, C. / Ghidelli-Disse, S. / Rullas, J. / Angulo-Barturen, I. / Singh, A. / Gurcha, S.S. / Nataraj, V. / Bethell, S. / Remuinan, M.J. / Encinas, L. / Jervis, P.J. / Cammack, N.C. / Bhatt, A. / Kruse, U. / Bantscheff, M. / Futterer, K. / Barros, D. / Ballell, L. / Drewes, G. / Besra, G.S.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Probable enoyl-CoA hydratase echA6
B: Probable enoyl-CoA hydratase echA6
C: Probable enoyl-CoA hydratase echA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8686
Polymers84,6913
Non-polymers1,1773
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-49 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 116.640, 171.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable enoyl-CoA hydratase echA6 / EchA6


Mass: 28230.186 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: echA6, Rv0905, MTCY31.33 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNP1, enoyl-CoA hydratase
#2: Chemical ChemComp-G59 / (5R,7R)-5-(4-ethylphenyl)-N-(4-fluorobenzyl)-7-methyl-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide


Mass: 392.469 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H25FN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.6 M tri-sodium citrate, cryoprotected by adding 10 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.61→85.9 Å / Num. all: 135533 / Num. obs: 31967 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/av σ(I): 8.7 / Net I/σ(I): 8.7
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE2

3he2


Resolution: 2.61→85.9 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.6 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 1612 5.05 %
Rwork0.1927 --
obs0.1951 31907 98.78 %
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.398 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9578 Å20 Å2-0 Å2
2--10.3634 Å20 Å2
3----8.4055 Å2
Refinement stepCycle: LAST / Resolution: 2.61→85.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5416 0 87 102 5605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095608
X-RAY DIFFRACTIONf_angle_d1.1267619
X-RAY DIFFRACTIONf_dihedral_angle_d15.5492027
X-RAY DIFFRACTIONf_chiral_restr0.069859
X-RAY DIFFRACTIONf_plane_restr0.0041008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6103-2.68710.30851390.26932490X-RAY DIFFRACTION99
2.6871-2.77390.34721300.27452497X-RAY DIFFRACTION100
2.7739-2.8730.32691330.26452496X-RAY DIFFRACTION100
2.873-2.98810.29121440.25152504X-RAY DIFFRACTION100
2.9881-3.12410.30291370.22452509X-RAY DIFFRACTION100
3.1241-3.28880.27741230.2162526X-RAY DIFFRACTION100
3.2888-3.49480.26631290.2092504X-RAY DIFFRACTION99
3.4948-3.76470.25331360.18982509X-RAY DIFFRACTION98
3.7647-4.14350.21711280.17952520X-RAY DIFFRACTION99
4.1435-4.74310.19941230.14132543X-RAY DIFFRACTION98
4.7431-5.97550.18161550.17352533X-RAY DIFFRACTION98
5.9755-85.94650.20361350.1662664X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.45-0.0782-0.56331.0679-0.05211.3127-0.12280.2669-0.3069-0.1352-0.04050.00260.326-0.1168-00.4377-0.0170.00570.4649-0.02870.447-12.776421.9986-28.4245
21.48670.6573-0.06441.1222-0.75511.57090.012-0.13960.370.3764-0.00250.2006-0.3814-0.1074-0.00020.510.05730.00270.4262-0.00530.4643-18.604348.5869-8.3851
31.5513-0.2878-0.33891.5974-0.03371.17620.03010.25930.2513-0.1416-0.0551-0.2347-0.21840.15580.00010.4217-0.0516-0.01360.55360.11620.46642.159951.769-35.3549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:243)
2X-RAY DIFFRACTION2(chain B and resseq 1:243)
3X-RAY DIFFRACTION3(chain C and resseq 1:243)

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