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- PDB-5dtp: Crystal structure of M. tuberculosis EchA6 (apo, trigonal crystal... -

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Basic information

Entry
Database: PDB / ID: 5dtp
TitleCrystal structure of M. tuberculosis EchA6 (apo, trigonal crystal form)
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
Probable enoyl-CoA hydratase EchA6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsCox, J.A.G. / Besra, G.S. / Futterer, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Union261378 United Kingdom
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


Theoretical massNumber of molelcules
Total (without water)84,4893
Polymers84,4893
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.120, 103.120, 143.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 250
2115B1 - 250
3115C1 - 250

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.502539, -0.204278, -0.840075), (0.225501, 0.907079, -0.355468), (0.834628, -0.368074, -0.409777)80.78642, -17.92671, -67.39784
3given(-0.495146, 0.229223, 0.838025), (-0.205517, 0.90629, -0.369325), (-0.844152, -0.355098, -0.401637)100.59647, 8.01284, 34.21481

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Components

#1: Protein Probable enoyl-CoA hydratase echA6


Mass: 28163.115 Da / Num. of mol.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl, 60% v/v polypropylene glycol 400 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→89.3 Å / Num. obs: 68929 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/av σ(I): 15.9 / Net I/σ(I): 15.9
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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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: 1.91→89.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.762 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20099 3508 5.1 %RANDOM
Rwork0.1822 ---
obs0.18315 65376 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.91→89.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5284 0 0 326 5610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.9557292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0395706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23623.904228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73215854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.151543
X-RAY DIFFRACTIONr_chiral_restr0.0680.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214093
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 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A904medium positional0.220.5
B904medium positional0.250.5
C904medium positional0.140.5
A778loose positional0.345
B778loose positional0.385
C778loose positional0.275
A904medium thermal3.082
B904medium thermal2.062
C904medium thermal2.882
A778loose thermal2.7110
B778loose thermal2.2210
C778loose thermal2.6710
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 248 -
Rwork0.25 4514 -
obs--100 %
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)
11.34390.0870.41221.10640.2541.5735-0.0111-0.23520.03150.21530.0461-0.1361-0.01260.1415-0.03490.14110.0276-0.05710.0928-0.01120.084272.6810.6923.696
21.22-0.1216-0.05341.03440.33871.77270.02120.2432-0.0311-0.16210.0205-0.15040.01290.1762-0.04170.11850.02540.01590.0811-0.00920.068767.192-7.724-28.663
31.5609-0.1443-0.20971.0222-0.07640.8803-0.0222-0.0514-0.02880.06490.04680.19430.0094-0.1872-0.02450.09170.01440.00580.06450.02760.065241.111-2.245-8.46
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 240
2X-RAY DIFFRACTION2B1 - 240
3X-RAY DIFFRACTION3C1 - 240

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