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- PDB-5duf: Crystal structure of M. tuberculosis EchA6 bound to ligand GSK729A -

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Basic information

Entry
Database: PDB / ID: 5duf
TitleCrystal structure of M. tuberculosis EchA6 bound to ligand GSK729A
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-G7A / Probable enoyl-CoA hydratase EchA6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)28,5692
Polymers28,2301
Non-polymers3391
Water4,882271
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)85,7086
Polymers84,6913
Non-polymers1,0183
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area8160 Å2
ΔGint-51 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.880, 103.880, 54.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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-G7A / (5R,7S)-5-(4-ethylphenyl)-7-(trifluoromethyl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxylic acid


Mass: 339.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16F3N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 10 % v/v polypropylene glycol

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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: 1.43→51.9 Å / Num. obs: 61860 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/av σ(I): 26.2 / Net I/σ(I): 26.2
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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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: 1.5→51.9 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 2705 5.04 %
Rwork0.1729 --
obs0.1734 53631 99.97 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.45 Å2 / ksol: 0.303 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0173 Å2-0 Å20 Å2
2---1.0173 Å2-0 Å2
3---2.0347 Å2
Refinement stepCycle: LAST / Resolution: 1.5→51.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 24 271 2096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061858
X-RAY DIFFRACTIONf_angle_d1.142526
X-RAY DIFFRACTIONf_dihedral_angle_d12.092668
X-RAY DIFFRACTIONf_chiral_restr0.064289
X-RAY DIFFRACTIONf_plane_restr0.004332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52730.28381510.24752627X-RAY DIFFRACTION100
1.5273-1.55670.26051430.24522673X-RAY DIFFRACTION100
1.5567-1.58850.24661440.21462635X-RAY DIFFRACTION100
1.5885-1.6230.22641500.20232693X-RAY DIFFRACTION100
1.623-1.66080.19971450.19632642X-RAY DIFFRACTION100
1.6608-1.70230.21391160.18552722X-RAY DIFFRACTION100
1.7023-1.74830.20311390.1822655X-RAY DIFFRACTION100
1.7483-1.79980.21541180.17192693X-RAY DIFFRACTION100
1.7998-1.85790.19151470.16972680X-RAY DIFFRACTION100
1.8579-1.92430.19231640.16732640X-RAY DIFFRACTION100
1.9243-2.00130.1821310.16932691X-RAY DIFFRACTION100
2.0013-2.09240.18791530.17422677X-RAY DIFFRACTION100
2.0924-2.20270.1841470.1682634X-RAY DIFFRACTION100
2.2027-2.34070.21121410.16542699X-RAY DIFFRACTION100
2.3407-2.52150.17031400.17152681X-RAY DIFFRACTION100
2.5215-2.77520.18131450.1712694X-RAY DIFFRACTION100
2.7752-3.17670.20781320.18132714X-RAY DIFFRACTION100
3.1767-4.00210.17141560.16932705X-RAY DIFFRACTION100
4.0021-51.97110.1411430.15572771X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -39.2879 Å / Origin y: 10.2115 Å / Origin z: -1.8948 Å
111213212223313233
T0.1317 Å20.0163 Å2-0.0125 Å2-0.0643 Å2-0.0091 Å2--0.1978 Å2
L1.1496 °20.0228 °2-0.311 °2-1.2926 °20.2435 °2--1.6356 °2
S-0.0472 Å °-0.0162 Å °-0.4779 Å °0.0704 Å °0.0759 Å °-0.356 Å °0.2619 Å °0.1517 Å °0.0008 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:143)

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