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- PDB-8an4: MenT1 toxin (rv0078a) from Mycobacterium tuberculosis H37Rv -

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Basic information

Entry
Database: PDB / ID: 8an4
TitleMenT1 toxin (rv0078a) from Mycobacterium tuberculosis H37Rv
ComponentsBacterial toxin
KeywordsTOXIN / Toxin-antitoxin Tuberculosis Nucleotidyltransferase MenT MenAT
Function / homologyNucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyltransferase superfamily / Nucleotidyl transferase AbiEii/AbiGii toxin family protein
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsXu, X. / Usher, B. / Gutierrez, C. / Barriot, R. / Arrowsmith, T.J. / Han, X. / Redder, P. / Neyrolles, O. / Blower, T.R. / Genevaux, P.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2023
Title: MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding.
Authors: Xu, X. / Usher, B. / Gutierrez, C. / Barriot, R. / Arrowsmith, T.J. / Han, X. / Redder, P. / Neyrolles, O. / Blower, T.R. / Genevaux, P.
History
DepositionAug 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterial toxin
B: Bacterial toxin


Theoretical massNumber of molelcules
Total (without water)43,0192
Polymers43,0192
Non-polymers00
Water2,162120
1
A: Bacterial toxin


Theoretical massNumber of molelcules
Total (without water)21,5091
Polymers21,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacterial toxin


Theoretical massNumber of molelcules
Total (without water)21,5091
Polymers21,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.988, 123.988, 118.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Bacterial toxin


Mass: 21509.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0078A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7N686
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 1.8 M lithium sulphate 0.1 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→43.84 Å / Num. obs: 55309 / % possible obs: 90.68 % / Redundancy: 102.3 % / Biso Wilson estimate: 36.95 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.95
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 5434 / CC1/2: 0.29

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Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: tbc

Resolution: 1.65→43.84 Å / SU ML: 0.2888 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5608
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2332 2316 4.62 %
Rwork0.2247 47851 -
obs0.2251 50167 90.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.87 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 0 120 3077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01342990
X-RAY DIFFRACTIONf_angle_d1.40824062
X-RAY DIFFRACTIONf_chiral_restr0.0708491
X-RAY DIFFRACTIONf_plane_restr0.0093538
X-RAY DIFFRACTIONf_dihedral_angle_d24.60661112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.734160.7583309X-RAY DIFFRACTION10.05
1.68-1.720.9284460.699861X-RAY DIFFRACTION28.33
1.72-1.760.60681340.56382847X-RAY DIFFRACTION92.12
1.76-1.80.50441440.49633082X-RAY DIFFRACTION99.91
1.8-1.850.47821550.43043101X-RAY DIFFRACTION99.94
1.85-1.90.36351610.35593053X-RAY DIFFRACTION99.78
1.9-1.970.28211660.32483084X-RAY DIFFRACTION99.75
1.97-2.040.27721580.27593097X-RAY DIFFRACTION99.94
2.04-2.120.26681730.25243070X-RAY DIFFRACTION99.94
2.12-2.210.221470.21373092X-RAY DIFFRACTION100
2.21-2.330.23591680.21383093X-RAY DIFFRACTION100
2.33-2.480.23121330.21223146X-RAY DIFFRACTION99.97
2.48-2.670.24371100.21343169X-RAY DIFFRACTION99.97
2.67-2.940.24811480.21633146X-RAY DIFFRACTION100
2.94-3.360.22671500.20853161X-RAY DIFFRACTION100
3.36-4.230.2081140.19443237X-RAY DIFFRACTION100
4.23-43.840.19341930.20533303X-RAY DIFFRACTION99.94

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