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- PDB-6wyi: Crystal structure of EchA19, enoyl-CoA hydratase from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 6wyi
TitleCrystal structure of EchA19, enoyl-CoA hydratase from Mycobacterium tuberculosis
ComponentsEchA19, enoyl-CoA hydratase
KeywordsLYASE / mycobacterium tuberculosis / cholesterol metabolism / enoyl-CoA hydratase
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / response to host immune response / cholesterol catabolic process / fatty acid beta-oxidation / lyase activity
Similarity search - Function
Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Enoyl-CoA hydratase EchA19
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.915 Å
AuthorsBonds, A.C. / Garcia-Diaz, M. / Sampson, N.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI134054 United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Post-translational Succinylation ofMycobacterium tuberculosisEnoyl-CoA Hydratase EchA19 Slows Catalytic Hydration of Cholesterol Catabolite 3-Oxo-chol-4,22-diene-24-oyl-CoA.
Authors: Bonds, A.C. / Yuan, T. / Werman, J.M. / Jang, J. / Lu, R. / Nesbitt, N.M. / Garcia-Diaz, M. / Sampson, N.S.
History
DepositionMay 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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: EchA19, enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5782
Polymers30,5541
Non-polymers241
Water1,35175
1
A: EchA19, enoyl-CoA hydratase
hetero molecules

A: EchA19, enoyl-CoA hydratase
hetero molecules

A: EchA19, enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7356
Polymers91,6623
Non-polymers733
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 area9920 Å2
ΔGint-85 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.413, 75.413, 68.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21A-427-

HOH

31A-471-

HOH

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Components

#1: Protein EchA19, enoyl-CoA hydratase


Mass: 30554.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: echA19, Rv3516 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O53561
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2 and 0.1 M Tris (pH 8.5) supplemented with 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.915→37.71 Å / Num. obs: 17862 / % possible obs: 99.88 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.08 / Net I/σ(I): 19.4
Reflection shellResolution: 1.915→1.983 Å / Rmerge(I) obs: 0.867 / Num. unique obs: 1755 / CC1/2: 0.931 / Rpim(I) all: 0.231 / Rrim(I) all: 0.898

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F47

4f47


Resolution: 1.915→37.71 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 861 4.82 %
Rwork0.1822 16984 -
obs0.1846 17862 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.41 Å2 / Biso mean: 56.3602 Å2 / Biso min: 28.23 Å2
Refinement stepCycle: final / Resolution: 1.915→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 1 75 1816
Biso mean--38.81 51.05 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011775
X-RAY DIFFRACTIONf_angle_d1.0352409
X-RAY DIFFRACTIONf_dihedral_angle_d16.186650
X-RAY DIFFRACTIONf_chiral_restr0.064281
X-RAY DIFFRACTIONf_plane_restr0.008319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.91-2.030.34581550.256727882943
2.03-2.190.27121360.214827622898
2.19-2.410.25111360.193228072943
2.41-2.760.25351370.185328302967
2.76-3.480.2361470.194728262973
3.48-37.710.20791500.163829713121
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)
15.18423.4797-1.33646.5459-0.67873.19410.1382-0.16261.35760.4391-0.1077-0.2317-0.47030.208-0.03750.5457-0.0137-0.15050.3547-0.02281.0703-38.185750.553384.7664
22.79660.501-4.41982.5975-0.28927.25610.1272-0.49750.81660.28460.03930.0367-0.22280.6204-0.08440.3603-0.0139-0.05130.4744-0.01530.7341-39.707141.344587.0307
35.7969-1.3320.98113.6722-0.51471.305-0.07920.28990.6167-0.0736-0.0704-0.3101-0.08190.17140.18230.2901-0.0178-0.05140.28960.04170.3467-29.961733.385380.274
44.5278-0.61530.18352.2512-0.90910.9756-0.1599-0.33230.34930.29070.07720.4996-0.1547-0.26280.06080.40550.010.03130.3841-0.1470.5659-55.999335.033989.5386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 92 )A2 - 92
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 109 )A93 - 109
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 190 )A110 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 263 )A191 - 263

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