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- PDB-6j7n: Crystal structure of toxin TglT (unusual type guanylyltransferase... -

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Basic information

Entry
Database: PDB / ID: 6j7n
TitleCrystal structure of toxin TglT (unusual type guanylyltransferase-like toxin, Rv1045) mutant D82A co-expressed with TakA from Mycobacterium tuberculosis
Componentsguanylyltransferase-like toxin
KeywordsTOXIN / guanylyltransferase / guanylyltransferase-like toxin / TA
Function / homologyNucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / nucleotide binding / metal ion binding / Nucleotidyl transferase AbiEii/AbiGii toxin family protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsYu, X. / Gao, X. / Zhu, K. / Wojdyla, J.A. / Wang, M. / Cui, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81572005 China
National Natural Science Foundation of China81401714 China
CitationJournal: Commun Biol / Year: 2020
Title: Characterization of a toxin-antitoxin system in Mycobacterium tuberculosis suggests neutralization by phosphorylation as the antitoxicity mechanism.
Authors: Yu, X. / Gao, X. / Zhu, K. / Yin, H. / Mao, X. / Wojdyla, J.A. / Qin, B. / Huang, H. / Wang, M. / Sun, Y.C. / Cui, S.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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: guanylyltransferase-like toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,49715
Polymers34,1571
Non-polymers34014
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.502, 95.502, 68.183
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein guanylyltransferase-like toxin


Mass: 34157.012 Da / Num. of mol.: 1 / Mutation: D82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv1045 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) / Strain (production host): BL21(DE3) / References: UniProt: P96356
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.63 Å3/Da / Density % sol: 53.19 % / Description: rod-like
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH=6.5, 0.2 M magnesium chloride hexahydrate and 25% polyethylene glycol 3,350 (v/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.29→47.75 Å / Num. obs: 29779 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 68.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.25
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 0.87 / Num. unique obs: 4746 / CC1/2: 0.478 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J7T

6j7t


Resolution: 2.294→47.75 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.81
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 1571 5.28 %Random
Rwork0.2112 ---
obs0.2141 29769 95.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 84.97 Å2
Refinement stepCycle: LAST / Resolution: 2.294→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 14 7 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072291
X-RAY DIFFRACTIONf_angle_d0.8323134
X-RAY DIFFRACTIONf_dihedral_angle_d14.0921402
X-RAY DIFFRACTIONf_chiral_restr0.046369
X-RAY DIFFRACTIONf_plane_restr0.006412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.294-2.3680.35521300.32352392X-RAY DIFFRACTION90
2.368-2.45270.33311680.29962714X-RAY DIFFRACTION100
2.4527-2.55080.35321360.28682674X-RAY DIFFRACTION100
2.5508-2.66690.32061280.27632711X-RAY DIFFRACTION100
2.6669-2.80750.28891480.2582658X-RAY DIFFRACTION99
2.8075-2.98340.3071450.26762650X-RAY DIFFRACTION98
2.9834-3.21370.35991620.26852593X-RAY DIFFRACTION99
3.2137-3.5370.3059820.24272283X-RAY DIFFRACTION82
3.537-4.04860.29221330.20582345X-RAY DIFFRACTION88
4.0486-5.09990.24031700.17412602X-RAY DIFFRACTION98
5.0999-47.76130.20561690.16822576X-RAY DIFFRACTION97

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