[English] 日本語
Yorodumi
- PDB-8an5: MenAT1 toxin-antitoxin complex (rv0078a-rv0078b) from Mycobacteri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8an5
TitleMenAT1 toxin-antitoxin complex (rv0078a-rv0078b) from Mycobacterium tuberculosis H37Rv
Components
  • Bacterial toxin
  • Conserved protein
KeywordsTOXIN / Toxin-antitoxin Tuberculosis Nucleotidyltransferase MenT MenAT
Function / homology
Function and homology information


Rv0078B-like antitoxin / Rv0078B-related antitoxin / Beta Polymerase; domain 2 - #40 / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Conserved protein / Nucleotidyl transferase AbiEii/AbiGii toxin family protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.44 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterial toxin
B: Bacterial toxin
C: Conserved protein


Theoretical massNumber of molelcules
Total (without water)50,4353
Polymers50,4353
Non-polymers00
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-33 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.868, 81.725, 64.826
Angle α, β, γ (deg.)90.000, 107.779, 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

-
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: Protein Conserved protein


Mass: 7416.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0078B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6X8G2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium fluoride 0.1 M Bis-Tris propane pH 6.5 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.44→43.68 Å / Num. obs: 82208 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 23.85 Å2 / CC1/2: 1 / Net I/σ(I): 13.07
Reflection shellResolution: 1.44→1.492 Å / Num. unique obs: 8166 / CC1/2: 0.63

-
Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.44→43.68 Å / SU ML: 0.1947 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1716
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1899 3895 4.75 %
Rwork0.1706 78182 -
obs0.1715 82077 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.7 Å2
Refinement stepCycle: LAST / Resolution: 1.44→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 344 3669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043374
X-RAY DIFFRACTIONf_angle_d1.12374577
X-RAY DIFFRACTIONf_chiral_restr0.2276546
X-RAY DIFFRACTIONf_plane_restr0.0077603
X-RAY DIFFRACTIONf_dihedral_angle_d18.62691261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.3741310.37062660X-RAY DIFFRACTION94.96
1.46-1.480.36521480.33542750X-RAY DIFFRACTION99.86
1.48-1.50.30121320.29652792X-RAY DIFFRACTION99.63
1.5-1.520.30151420.26992784X-RAY DIFFRACTION99.93
1.52-1.540.27671560.24692780X-RAY DIFFRACTION99.9
1.54-1.560.30981350.24852804X-RAY DIFFRACTION99.9
1.56-1.580.27381390.23222803X-RAY DIFFRACTION99.93
1.58-1.610.30211440.22462734X-RAY DIFFRACTION99.86
1.61-1.640.27411260.22612823X-RAY DIFFRACTION99.9
1.64-1.670.26741410.21132761X-RAY DIFFRACTION99.86
1.67-1.70.23991330.19452819X-RAY DIFFRACTION99.86
1.7-1.730.22881410.18272762X-RAY DIFFRACTION99.9
1.73-1.770.19581440.16842795X-RAY DIFFRACTION100
1.77-1.810.18731490.16282783X-RAY DIFFRACTION100
1.81-1.860.18591520.15662795X-RAY DIFFRACTION100
1.86-1.910.18931290.15812809X-RAY DIFFRACTION100
1.91-1.970.20441390.16862784X-RAY DIFFRACTION99.93
1.97-2.030.19921260.1632818X-RAY DIFFRACTION99.97
2.03-2.10.16661270.15952805X-RAY DIFFRACTION100
2.1-2.190.19491550.16212778X-RAY DIFFRACTION100
2.19-2.290.21941650.1582772X-RAY DIFFRACTION100
2.29-2.410.16661480.14812807X-RAY DIFFRACTION100
2.41-2.560.19881300.15762810X-RAY DIFFRACTION100
2.56-2.750.1771230.16592798X-RAY DIFFRACTION100
2.75-3.030.20911280.17092842X-RAY DIFFRACTION100
3.03-3.470.16161350.15992824X-RAY DIFFRACTION100
3.47-4.370.15051430.14862824X-RAY DIFFRACTION100
4.37-43.680.17351340.17972866X-RAY DIFFRACTION99.37

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more