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- PDB-6ldz: Crystal structure of Rv0222 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6ldz
TitleCrystal structure of Rv0222 from Mycobacterium tuberculosis
ComponentsProbable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)
KeywordsLYASE / hydratase
Function / homology
Function and homology information


enoyl-CoA hydratase activity / fatty acid beta-oxidation
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / 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 ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, J. / Ran, Y.J. / Wang, L. / Wu, J.H. / Ge, B.X. / Rao, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFC0840300 China
CitationJournal: Nature / Year: 2020
Title: Host-mediated ubiquitination of a mycobacterial protein suppresses immunity.
Authors: Wang, L. / Wu, J. / Li, J. / Yang, H. / Tang, T. / Liang, H. / Zuo, M. / Wang, J. / Liu, H. / Liu, F. / Chen, J. / Liu, Z. / Wang, Y. / Peng, C. / Wu, X. / Zheng, R. / Huang, X. / Ran, Y. / Rao, Z. / Ge, B.
History
DepositionNov 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)


Theoretical massNumber of molelcules
Total (without water)27,4521
Polymers27,4521
Non-polymers00
Water99155
1
A: Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)

A: Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)

A: Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)


Theoretical massNumber of molelcules
Total (without water)82,3573
Polymers82,3573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
Buried area8820 Å2
ΔGint-76 kcal/mol
Surface area29900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.626, 120.626, 120.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)


Mass: 27452.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: echA1, Rv0222 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P96404
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 3.5 M Sodium formate, pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.4→85.295 Å / Num. obs: 11608 / % possible obs: 100 % / Redundancy: 20 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.098 / Rsym value: 0.096 / Net I/av σ(I): 7.7 / Net I/σ(I): 28.1 / Num. measured all: 231881
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.53200.651.23416017080.1480.6670.655.5100
2.53-2.6819.90.4571.73130415730.1040.4690.4577.7100
2.68-2.8720.80.3392.33068914740.0760.3480.33910.2100
2.87-3.119.80.2293.42761113920.0520.2350.22914.7100
3.1-3.3920.10.1395.42570912810.0320.1430.13923.1100
3.39-3.7920.40.0868.62385311670.0190.0880.08638100
3.79-4.3819.30.05114.22006110390.0120.0530.05157.6100
4.38-5.3720.50.04217180228810.010.0430.04265.8100
5.37-7.5919.10.0418132116920.0090.0410.0459.3100
7.59-42.64818.10.02330.372614010.0050.0240.02389.999.5

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qxi

3qxi


Resolution: 2.4→42.648 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.63
RfactorNum. reflection% reflection
Rfree0.2287 560 4.82 %
Rwork0.1765 --
obs0.1792 11607 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.24 Å2 / Biso mean: 44.6722 Å2 / Biso min: 21.4 Å2
Refinement stepCycle: final / Resolution: 2.4→42.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 0 55 1894
Biso mean---43.83 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081866
X-RAY DIFFRACTIONf_angle_d0.7922532
X-RAY DIFFRACTIONf_chiral_restr0.051298
X-RAY DIFFRACTIONf_plane_restr0.006335
X-RAY DIFFRACTIONf_dihedral_angle_d13.4471135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4001-2.64160.28591360.1982737
2.6416-3.02370.24811370.19312737
3.0237-3.80920.26551210.1742759
3.8092-42.6480.19971660.16772814
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)
10.6734-0.2359-0.27830.50250.7240.99150.151-0.50110.14910.34040.0692-0.3269-0.2656-0.0051-0.00240.2741-0.1009-0.03050.41410.0290.363449.9998101.9407114.6483
21.70790.25750.49130.618-0.79422.62660.0543-0.4545-0.06630.2385-0.2250.0484-0.20050.1024-0.0010.4069-0.0717-0.00110.4120.01970.330643.005897.2618117.8623
30.84990.70660.72330.5880.37441.02950.0089-0.24760.22311.51990.16810.3697-0.702-0.3871-0.00340.625-0.09090.09130.57810.02710.549633.691692.5239127.5158
41.54021.18110.89350.9010.55911.46550.062-0.23680.04020.288-0.2047-0.0181-0.1399-0.2371-0.00190.3086-0.01830.02040.31910.02230.242336.77596.9901110.8203
50.4013-0.0535-0.34220.3065-0.0760.22460.37370.06280.1329-0.2264-0.2616-0.0117-0.2024-0.0920.00040.3118-0.011-0.00180.32410.05240.286429.828186.8717111.6305
60.45170.25140.04160.2407-0.32921.1267-0.40550.10210.1163-0.15190.5552-0.08790.0748-0.354300.3416-0.0331-0.08060.3490.07170.292923.73289.7887103.7861
70.42390.06340.32480.36550.41590.61050.1489-0.0427-0.4473-0.3061-0.0928-0.03160.16980.23560.0030.3431-0.0480.0040.3654-0.01140.321932.767985.3402100.2782
80.2916-0.47180.68521.174-0.76061.5192-0.05010.0088-0.027-0.0057-0.0697-0.095-0.07390.0346-0.00010.286-0.04370.01960.33270.04180.33541.199104.1549102.0585
90.18030.0869-0.09030.4286-0.53970.46330.01020.05390.12840.36210.12860.5386-0.1467-0.53250.01140.56080.0415-0.01870.6030.01840.535824.1059117.5522102.6143
100.30030.7919-0.07092.3776-0.02562.04620.1185-0.55730.19880.3372-0.1078-0.5761-0.11821.0156-0.01210.3824-0.0024-0.0740.37820.03810.496247.0361123.50296.8247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 27 )A12 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 74 )A28 - 74
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 90 )A75 - 90
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 127 )A91 - 127
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 150 )A128 - 150
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 165 )A151 - 165
7X-RAY DIFFRACTION7chain 'A' and (resid 166 through 178 )A166 - 178
8X-RAY DIFFRACTION8chain 'A' and (resid 179 through 218 )A179 - 218
9X-RAY DIFFRACTION9chain 'A' and (resid 219 through 239 )A219 - 239
10X-RAY DIFFRACTION10chain 'A' and (resid 240 through 262 )A240 - 262

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