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- PDB-5du8: Crystal structure of M. tuberculosis EchA6 bound to GSK572A -

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Basic information

Entry
Database: PDB / ID: 5du8
TitleCrystal structure of M. tuberculosis EchA6 bound to GSK572A
ComponentsProbable enoyl-CoA hydratase echA6
KeywordsLIPID BINDING PROTEIN / lyase / 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-5FK / Probable enoyl-CoA hydratase EchA6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)86,0336
Polymers84,6913
Non-polymers1,3423
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.390, 115.980, 171.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA1 - 5921 - 79
21METMETGLYGLYBB1 - 5921 - 79
31METMETGLYGLYCC1 - 5921 - 79
12ASPASPALAALAAA73 - 24393 - 263
22ASPASPALAALABB73 - 24393 - 263
32ASPASPALAALACC73 - 24393 - 263

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.406254, -0.801214, 0.439333), (0.185299, -0.398571, -0.898223), (0.894775, 0.446315, -0.013457)37.41028, 36.88296, -33.97377
3given(0.413625, 0.191228, 0.890138), (-0.794937, -0.400763, 0.455483), (0.443836, -0.896003, -0.013751)8.08462, 60.31478, 16.13243

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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-5FK / (5R,7S)-5-(4-ethylphenyl)-N-[(5-fluoropyridin-2-yl)methyl]-7-(trifluoromethyl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide


Mass: 447.429 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H21F4N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium chloride, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate, cryoprotected adding a 10 % ethylene glycol
PH range: 6.5

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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: May 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.23→96.1 Å / Num. obs: 50922 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 11.9
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE2

3he2


Resolution: 2.23→96.07 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.655 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25368 2580 5.1 %RANDOM
Rwork0.21988 ---
obs0.22157 48273 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.413 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0 Å2
2--2.36 Å20 Å2
3----1.25 Å2
Refinement stepCycle: 1 / Resolution: 2.23→96.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 96 166 5606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9797530
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7123.87230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73815872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7741545
X-RAY DIFFRACTIONr_chiral_restr0.0770.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214227
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1715 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.320.5
Bmedium positional0.260.5
Cmedium positional0.350.5
Amedium thermal2.272
Bmedium thermal2.592
Cmedium thermal2.182
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 182 -
Rwork0.329 3235 -
obs--99.74 %
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)
11.20780.0348-0.70561.313-0.00512.3955-0.16050.2472-0.313-0.1591-0.00770.00120.4402-0.06960.16820.1007-0.02110.0370.2499-0.0210.091-12.42622.093-28.094
21.71320.9454-0.22731.9374-0.58711.31280.0655-0.11860.36980.3372-0.01110.2249-0.35-0.1618-0.05440.1190.04860.02010.19540.0170.091-18.11548.458-8.419
31.7197-0.1492-0.38551.78190.14591.45840.0020.34330.315-0.20260.0879-0.221-0.3520.165-0.08990.1074-0.06340.02680.31330.11540.10142.35351.469-35.325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 243
2X-RAY DIFFRACTION2B1 - 243
3X-RAY DIFFRACTION3C1 - 243

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