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- PDB-5dtw: Crystal structure of M. tuberculosis EchA6 bound to C20-CoA -

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Basic information

Entry
Database: PDB / ID: 5dtw
TitleCrystal structure of M. tuberculosis EchA6 bound to C20-CoA
Componentsenoyl-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
Arachinoyl-CoA / Probable enoyl-CoA hydratase EchA6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.439 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: enoyl-CoA hydratase echA6
B: enoyl-CoA hydratase echA6
C: enoyl-CoA hydratase echA6
D: enoyl-CoA hydratase echA6
E: enoyl-CoA hydratase echA6
F: enoyl-CoA hydratase echA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,5058
Polymers169,3816
Non-polymers2,1242
Water2,180121
1
A: enoyl-CoA hydratase echA6
B: enoyl-CoA hydratase echA6
C: enoyl-CoA hydratase echA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7534
Polymers84,6913
Non-polymers1,0621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-54 kcal/mol
Surface area27690 Å2
MethodPISA
2
D: enoyl-CoA hydratase echA6
E: enoyl-CoA hydratase echA6
F: enoyl-CoA hydratase echA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7534
Polymers84,6913
Non-polymers1,0621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-55 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.603, 51.275, 156.825
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
enoyl-CoA hydratase echA6


Mass: 28230.186 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: echA6, Rv0905, MTCY31.33 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNP1, enoyl-CoA hydratase
#2: Chemical ChemComp-5F9 / Arachinoyl-CoA


Mass: 1062.049 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H74N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.17 M ammonium sulfate, 25.5 % w/v PEG 4000, 15 % v/v 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: 2.4→108.9 Å / Num. all: 246225 / Num. obs: 68420 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/av σ(I): 9.6 / Net I/σ(I): 9.6
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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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: 2.439→42.848 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2749 3255 5.06 %
Rwork0.2218 --
obs0.2245 64285 98.43 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.26 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3317 Å20 Å25.8651 Å2
2--6.8418 Å20 Å2
3----6.5102 Å2
Refinement stepCycle: LAST / Resolution: 2.439→42.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10792 0 138 121 11051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811123
X-RAY DIFFRACTIONf_angle_d1.20215112
X-RAY DIFFRACTIONf_dihedral_angle_d15.0334039
X-RAY DIFFRACTIONf_chiral_restr0.0741717
X-RAY DIFFRACTIONf_plane_restr0.0051992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4392-2.47560.34731300.31312570X-RAY DIFFRACTION99
2.4756-2.51430.37321430.29482648X-RAY DIFFRACTION98
2.5143-2.55550.34231390.27932666X-RAY DIFFRACTION99
2.5555-2.59950.33961470.27012611X-RAY DIFFRACTION98
2.5995-2.64680.33071480.26432630X-RAY DIFFRACTION98
2.6468-2.69770.3171480.26032612X-RAY DIFFRACTION97
2.6977-2.75270.32121270.25252601X-RAY DIFFRACTION98
2.7527-2.81260.31121320.24172659X-RAY DIFFRACTION99
2.8126-2.8780.31251320.25572665X-RAY DIFFRACTION99
2.878-2.950.35061670.25782588X-RAY DIFFRACTION98
2.95-3.02970.321380.25912650X-RAY DIFFRACTION98
3.0297-3.11880.31291270.25442631X-RAY DIFFRACTION99
3.1188-3.21950.29851180.25572700X-RAY DIFFRACTION99
3.2195-3.33450.29861530.24052609X-RAY DIFFRACTION99
3.3345-3.46790.28631510.23832664X-RAY DIFFRACTION98
3.4679-3.62570.29471390.21582633X-RAY DIFFRACTION98
3.6257-3.81670.28221520.22442649X-RAY DIFFRACTION99
3.8167-4.05570.21991440.18822657X-RAY DIFFRACTION98
4.0557-4.36860.23441210.16782695X-RAY DIFFRACTION98
4.3686-4.80770.20551610.15252635X-RAY DIFFRACTION98
4.8077-5.50210.24651410.18682715X-RAY DIFFRACTION99
5.5021-6.92730.22481410.19822728X-RAY DIFFRACTION99
6.9273-42.85480.18831560.17542814X-RAY DIFFRACTION98
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)
10.73010.07220.17550.8151-0.05060.63740.0970.14350.037-0.1525-0.048-0.09790.01530.08460.0490.08060.00190.0034-0.06060.010.0947-30.4115-9.379-12.8889
21.0936-0.1081-0.07270.64770.08220.68850.0719-0.19480.0540.14260.01330.00990.11710.02060.05520.05680.0094-0.05310.0736-0.01220.0635-19.4259-23.8588-49.2335
30.86550.31790.26350.7229-0.02880.4434-0.01750.4263-0.0973-0.28040.0239-0.06860.10410.1246-0.03320.20050.1208-0.04250.3195-0.03980.0409-14.1639-28.3303-82.2825
40.9698-0.04280.04441.1419-0.21140.4278-0.1402-0.395-0.15530.24120.0155-0.11250.12540.1741-0.07110.20330.1075-0.02460.17350.05950.1898-17.6605-23.759914.6709
50.9603-0.1126-0.04020.6079-0.00110.3417-0.0965-0.47960.12060.34310.10760.0966-0.0996-0.01130.01240.21820.080.05650.168-0.04620.1102-44.44-3.473117.2536
60.84280.20310.14151.1328-0.01490.5050.07490.12520.1585-0.1382-0.0025-0.1912-0.13680.30980.04330.0765-0.00630.02890.22380.01020.19227.7501-10.06-64.0441
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)
4X-RAY DIFFRACTION4(chain D and resseq 1:243)
5X-RAY DIFFRACTION5(chain E and resseq 1:243)
6X-RAY DIFFRACTION6(chain F and resseq 1:243)

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