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- PDB-5du4: Crystal structure of M. tuberculosis EchA6 bound to ligand GSK366A -

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Basic information

Entry
Database: PDB / ID: 5du4
TitleCrystal structure of M. tuberculosis EchA6 bound to ligand GSK366A
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-5FF / Probable enoyl-CoA hydratase EchA6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 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

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Assembly

Deposited unit
A: Probable enoyl-CoA hydratase echA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6892
Polymers28,2301
Non-polymers4581
Water1,69394
1
A: Probable enoyl-CoA hydratase echA6
hetero molecules

A: Probable enoyl-CoA hydratase echA6
hetero molecules

A: Probable enoyl-CoA hydratase echA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0666
Polymers84,6913
Non-polymers1,3753
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8390 Å2
ΔGint-50 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.830, 94.830, 87.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 28230.186 Da / Num. of mol.: 1
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-5FF / (5R,7S)-5-(4-ethylphenyl)-N-(4-methoxybenzyl)-7-(trifluoromethyl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide


Mass: 458.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25F3N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 20 % v/v ethanol / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→47.4 Å / Num. obs: 31804 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/av σ(I): 12.6 / Net I/σ(I): 12.6
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 99.3

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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: 1.702→47.4 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.35 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 1604 5.04 %
Rwork0.1932 --
obs0.1943 31794 98.83 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.056 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0934 Å2-0 Å20 Å2
2---0.0934 Å2-0 Å2
3---0.1868 Å2
Refinement stepCycle: LAST / Resolution: 1.702→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 33 94 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061867
X-RAY DIFFRACTIONf_angle_d1.1972538
X-RAY DIFFRACTIONf_dihedral_angle_d12.637673
X-RAY DIFFRACTIONf_chiral_restr0.071288
X-RAY DIFFRACTIONf_plane_restr0.004333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7023-1.75720.32231520.29882757X-RAY DIFFRACTION99
1.7572-1.820.26351550.24342817X-RAY DIFFRACTION100
1.82-1.89290.25361600.21562716X-RAY DIFFRACTION100
1.8929-1.9790.29121240.24822737X-RAY DIFFRACTION98
1.979-2.08340.22341450.19432776X-RAY DIFFRACTION100
2.0834-2.21390.24661460.18962795X-RAY DIFFRACTION100
2.2139-2.38480.21891440.19672740X-RAY DIFFRACTION99
2.3848-2.62480.20261520.19062705X-RAY DIFFRACTION99
2.6248-3.00460.21391460.20362719X-RAY DIFFRACTION97
3.0046-3.78520.22691470.20462740X-RAY DIFFRACTION98
3.7852-47.43340.17671330.16162688X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -15.868 Å / Origin y: 11.4495 Å / Origin z: 27.9174 Å
111213212223313233
T0.1976 Å20.0436 Å2-0.0227 Å2-0.2408 Å2-0.0209 Å2--0.2327 Å2
L1.1966 °20.4603 °20.0871 °2-1.8636 °20.0882 °2--1.0752 °2
S-0.028 Å °0.027 Å °0.2763 Å °-0.0255 Å °-0.0475 Å °0.4099 Å °-0.2022 Å °-0.2315 Å °-0.0055 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:243)

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