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- PDB-6y56: MenT4, nucleotidyltransferase toxin Rv2826c from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 6y56
TitleMenT4, nucleotidyltransferase toxin Rv2826c from Mycobacterium tuberculosis H37Rv
ComponentsUncharacterized protein
KeywordsTOXIN / Nucleotidyltransferase Toxin-antitoxin system Tuberculosis
Function / homologyNucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / plasma membrane / Nucleotidyl transferase AbiEii/AbiGii toxin family protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.23 Å
AuthorsUsher, B. / Blower, T.R.
CitationJournal: Sci Adv / Year: 2020
Title: A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems.
Authors: Cai, Y. / Usher, B. / Gutierrez, C. / Tolcan, A. / Mansour, M. / Fineran, P.C. / Condon, C. / Neyrolles, O. / Genevaux, P. / Blower, T.R.
History
DepositionFeb 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 20, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)33,0081
Polymers33,0081
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13280 Å2
Unit cell
Length a, b, c (Å)42.268, 57.804, 54.734
Angle α, β, γ (deg.)90.000, 92.293, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Uncharacterized protein


Mass: 33007.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv2826c / Production host: Escherichia coli (E. coli) / References: UniProt: P71626
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium Acetate Hydrate 0.1 M Tris pH 8.5 25% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9781 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 1.23→54.69 Å / Num. obs: 75996 / % possible obs: 98.8 % / Redundancy: 1.97 % / Biso Wilson estimate: 15.55 Å2 / CC1/2: 0.996 / Net I/σ(I): 15.55
Reflection shellResolution: 1.23→1.274 Å / Num. unique obs: 7206 / CC1/2: 0.294

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.23→54.69 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.6412
RfactorNum. reflection% reflection
Rfree0.195 3598 4.77 %
Rwork0.184 --
obs0.1845 75481 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.58 Å2
Refinement stepCycle: LAST / Resolution: 1.23→54.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 0 327 2649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532368
X-RAY DIFFRACTIONf_angle_d0.82863209
X-RAY DIFFRACTIONf_chiral_restr0.0712356
X-RAY DIFFRACTIONf_plane_restr0.0049424
X-RAY DIFFRACTIONf_dihedral_angle_d19.2346878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.250.32591340.32912262X-RAY DIFFRACTION82.65
1.25-1.260.35081220.31662557X-RAY DIFFRACTION91.15
1.26-1.280.3231400.30082758X-RAY DIFFRACTION97.09
1.28-1.30.28551390.28462714X-RAY DIFFRACTION99.3
1.3-1.320.29261360.27312782X-RAY DIFFRACTION99.39
1.32-1.340.27911470.26962720X-RAY DIFFRACTION99.41
1.34-1.370.27171650.26032796X-RAY DIFFRACTION99.9
1.37-1.390.24531490.25242755X-RAY DIFFRACTION100
1.39-1.420.2551530.2452788X-RAY DIFFRACTION99.97
1.42-1.450.26731390.22892782X-RAY DIFFRACTION99.97
1.45-1.480.24271360.21062794X-RAY DIFFRACTION99.97
1.48-1.510.23111000.20092825X-RAY DIFFRACTION100
1.51-1.550.21961250.19582789X-RAY DIFFRACTION100
1.55-1.590.21021380.18572812X-RAY DIFFRACTION100
1.59-1.640.20721490.18472778X-RAY DIFFRACTION100
1.64-1.690.19411260.19222832X-RAY DIFFRACTION100
1.69-1.750.2221220.17962814X-RAY DIFFRACTION100
1.75-1.820.20871420.18882779X-RAY DIFFRACTION100
1.82-1.90.19641600.1822779X-RAY DIFFRACTION100
1.9-2.010.18481450.17292788X-RAY DIFFRACTION100
2.01-2.130.18311200.16982837X-RAY DIFFRACTION100
2.13-2.30.18721500.16672785X-RAY DIFFRACTION100
2.3-2.530.19861670.17182781X-RAY DIFFRACTION100
2.53-2.890.16471310.17652830X-RAY DIFFRACTION100
2.89-3.640.16921230.16872855X-RAY DIFFRACTION100
3.64-54.690.15761400.16192891X-RAY DIFFRACTION99.97

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