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- PDB-5duc: Crystal structure of M. tuberculosis EchA6 bound to ligand GSK951A -

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Basic information

Entry
Database: PDB / ID: 5duc
TitleCrystal structure of M. tuberculosis EchA6 bound to ligand GSK951A
ComponentsProbable enoyl-CoA hydratase echA6
KeywordsLIPID BINDING PROTEIN / enoyl-CoA hydratase-like / lyase
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-G51 / Probable enoyl-CoA hydratase EchA6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.704 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)86,1086
Polymers84,6913
Non-polymers1,4173
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-53 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.340, 119.230, 171.620
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


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-G51 / (5R,7S)-N-(1,3-benzodioxol-5-ylmethyl)-5-(4-ethylphenyl)-7-(trifluoromethyl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide


Mass: 472.460 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H23F3N4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 1.0 M tri-sodium citrate, cryoprotected adding 20 % glycerol
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→48.9 Å / Num. obs: 29564 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/av σ(I): 25.8 / Net I/σ(I): 25.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 7.3 / % possible all: 97.5

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Processing

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

3he2


Resolution: 2.704→48.9 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1501 5.09 %
Rwork0.1872 --
obs0.1896 29498 99.51 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.035 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7828 Å20 Å2-0 Å2
2---1.2136 Å20 Å2
3----2.5692 Å2
Refinement stepCycle: LAST / Resolution: 2.704→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5452 0 102 109 5663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095661
X-RAY DIFFRACTIONf_angle_d1.3787698
X-RAY DIFFRACTIONf_dihedral_angle_d15.5672058
X-RAY DIFFRACTIONf_chiral_restr0.068864
X-RAY DIFFRACTIONf_plane_restr0.0051015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7044-2.79170.32081190.24472366X-RAY DIFFRACTION96
2.7917-2.89150.30211480.23742511X-RAY DIFFRACTION100
2.8915-3.00730.32381440.2412521X-RAY DIFFRACTION100
3.0073-3.14410.31151260.22442527X-RAY DIFFRACTION100
3.1441-3.30980.30391530.22172505X-RAY DIFFRACTION100
3.3098-3.51710.23951450.20062530X-RAY DIFFRACTION100
3.5171-3.78860.20021280.18792528X-RAY DIFFRACTION100
3.7886-4.16970.1861420.16672577X-RAY DIFFRACTION100
4.1697-4.77260.18761170.1372603X-RAY DIFFRACTION100
4.7726-6.01130.19761380.17242600X-RAY DIFFRACTION100
6.0113-48.96740.18361410.15212729X-RAY DIFFRACTION99
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)
11.1067-0.32920.61740.7567-0.14721.4611-0.09520.14020.2694-0.0736-0.0584-0.042-0.29060.1576-0.00410.1744-0.0142-0.01070.15560.00910.2295-13.333838.0579-28.1604
21.04170.78610.27581.23130.51521.31950.1005-0.1149-0.2090.2353-0.032-0.20790.35560.14410.0060.22030.0457-0.03080.19560.01010.1713-7.753510.5958-8.9349
30.9146-0.30310.25621.7042-0.03131.0740.04620.1136-0.1085-0.20160.02910.18240.2578-0.21610.00340.1793-0.033-0.04750.2386-0.03480.1862-28.25768.4215-35.8729
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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