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- PDB-6j7p: Crystal structure of toxin TglT (unusual type guanylyltransferase... -

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Basic information

Entry
Database: PDB / ID: 6j7p
TitleCrystal structure of toxin TglT (unusual type guanylyltransferase-like toxin, Rv1045) mutant E146Q 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: 2.629 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 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)34,3534
Polymers34,2801
Non-polymers733
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.691, 94.691, 67.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-301-

MG

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Components

#1: Protein guanylyltransferase-like toxin


Mass: 34280.016 Da / Num. of mol.: 1 / Mutation: E146Q
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.: 3 / 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
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M magnesium chloride hexahydrate, 0.1M bis-tris ph6.5, 25% PEG 3350, 10% ethylene glycol

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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: 2.61→47.34 Å / Num. obs: 18280 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Redundancy: 2.47 % / Biso Wilson estimate: 55.2 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.149 / Net I/σ(I): 4.45
Reflection shellResolution: 2.61→2.77 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 2487 / CC1/2: 0.808 / % possible all: 75.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.629→47.34 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.87
RfactorNum. reflection% reflection
Rfree0.2945 461 4.64 %
Rwork0.2719 --
obs0.273 9935 93.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.629→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 3 7 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042244
X-RAY DIFFRACTIONf_angle_d0.5983065
X-RAY DIFFRACTIONf_dihedral_angle_d16.7371360
X-RAY DIFFRACTIONf_chiral_restr0.042360
X-RAY DIFFRACTIONf_plane_restr0.004401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6294-3.00980.39911560.38523124X-RAY DIFFRACTION94
3.0098-3.79180.39571320.31753084X-RAY DIFFRACTION91
3.7918-47.35320.22821730.22443266X-RAY DIFFRACTION95

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