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- PDB-6j7q: Crystal structure of toxin TglT (unusual type guanylyltransferase... -

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Basic information

Entry
Database: PDB / ID: 6j7q
TitleCrystal structure of toxin TglT (unusual type guanylyltransferase-like toxin, Rv1045) mutant S78A 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: 1.85 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)34,64416
Polymers34,1851
Non-polymers45915
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-126 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.413, 95.413, 68.129
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: 34185.023 Da / Num. of mol.: 1 / Mutation: S78A
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) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P96356
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2M magnesium chloride hexahydrate, 0.1M bis-tris ph 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.85→39.08 Å / Num. obs: 30873 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.98 % / Biso Wilson estimate: 41.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Net I/σ(I): 22.42
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 10.12 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 4918 / CC1/2: 0.855 / % possible all: 99.5

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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: 1.85→39.078 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1517 4.91 %Random
Rwork0.1939 ---
obs0.1952 30867 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→39.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 15 202 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092283
X-RAY DIFFRACTIONf_angle_d0.8433122
X-RAY DIFFRACTIONf_dihedral_angle_d13.9661394
X-RAY DIFFRACTIONf_chiral_restr0.057367
X-RAY DIFFRACTIONf_plane_restr0.007411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8502-1.90990.33451470.30172615X-RAY DIFFRACTION99
1.9099-1.97820.2731380.25642643X-RAY DIFFRACTION100
1.9782-2.05740.2511480.23132635X-RAY DIFFRACTION100
2.0574-2.1510.25251340.21612618X-RAY DIFFRACTION100
2.151-2.26440.2481000.21332684X-RAY DIFFRACTION100
2.2644-2.40630.25771340.20972662X-RAY DIFFRACTION100
2.4063-2.5920.23161250.20742669X-RAY DIFFRACTION100
2.592-2.85280.23561560.21332661X-RAY DIFFRACTION100
2.8528-3.26540.23551330.20242681X-RAY DIFFRACTION100
3.2654-4.11340.21821400.17712695X-RAY DIFFRACTION100
4.1134-39.0870.18081620.16652787X-RAY DIFFRACTION100

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