[English] 日本語
Yorodumi
- PDB-6y56: MenT4, nucleotidyltransferase toxin Rv2826c from Mycobacterium tu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y56
TitleMenT4, nucleotidyltransferase toxin Rv2826c from Mycobacterium tuberculosis H37Rv
ComponentsUncharacterized protein
KeywordsTOXIN / Nucleotidyltransferase Toxin-antitoxin system Tuberculosis
Function / homologyNucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / plasma membrane / Uncharacterized protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.23 Å
AuthorsUsher, B. / Blower, T.R.
CitationJournal: Sci Adv / Year: 2020
Title: A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems.
Authors: Cai, Y. / Usher, B. / Gutierrez, C. / Tolcan, A. / Mansour, M. / Fineran, P.C. / Condon, C. / Neyrolles, O. / Genevaux, P. / Blower, T.R.
History
DepositionFeb 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 20, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)33,0081
Polymers33,0081
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13280 Å2
Unit cell
Length a, b, c (Å)42.268, 57.804, 54.734
Angle α, β, γ (deg.)90.000, 92.293, 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 Uncharacterized protein


Mass: 33007.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv2826c / Production host: Escherichia coli (E. coli) / References: UniProt: P71626
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium Acetate Hydrate 0.1 M Tris pH 8.5 25% w/v PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9781 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 1.23→54.69 Å / Num. obs: 75996 / % possible obs: 98.8 % / Redundancy: 1.97 % / Biso Wilson estimate: 15.55 Å2 / CC1/2: 0.996 / Net I/σ(I): 15.55
Reflection shellResolution: 1.23→1.274 Å / Num. unique obs: 7206 / CC1/2: 0.294

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.23→54.69 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.6412
RfactorNum. reflection% reflection
Rfree0.195 3598 4.77 %
Rwork0.184 --
obs0.1845 75481 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.58 Å2
Refinement stepCycle: LAST / Resolution: 1.23→54.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 0 327 2649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532368
X-RAY DIFFRACTIONf_angle_d0.82863209
X-RAY DIFFRACTIONf_chiral_restr0.0712356
X-RAY DIFFRACTIONf_plane_restr0.0049424
X-RAY DIFFRACTIONf_dihedral_angle_d19.2346878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.250.32591340.32912262X-RAY DIFFRACTION82.65
1.25-1.260.35081220.31662557X-RAY DIFFRACTION91.15
1.26-1.280.3231400.30082758X-RAY DIFFRACTION97.09
1.28-1.30.28551390.28462714X-RAY DIFFRACTION99.3
1.3-1.320.29261360.27312782X-RAY DIFFRACTION99.39
1.32-1.340.27911470.26962720X-RAY DIFFRACTION99.41
1.34-1.370.27171650.26032796X-RAY DIFFRACTION99.9
1.37-1.390.24531490.25242755X-RAY DIFFRACTION100
1.39-1.420.2551530.2452788X-RAY DIFFRACTION99.97
1.42-1.450.26731390.22892782X-RAY DIFFRACTION99.97
1.45-1.480.24271360.21062794X-RAY DIFFRACTION99.97
1.48-1.510.23111000.20092825X-RAY DIFFRACTION100
1.51-1.550.21961250.19582789X-RAY DIFFRACTION100
1.55-1.590.21021380.18572812X-RAY DIFFRACTION100
1.59-1.640.20721490.18472778X-RAY DIFFRACTION100
1.64-1.690.19411260.19222832X-RAY DIFFRACTION100
1.69-1.750.2221220.17962814X-RAY DIFFRACTION100
1.75-1.820.20871420.18882779X-RAY DIFFRACTION100
1.82-1.90.19641600.1822779X-RAY DIFFRACTION100
1.9-2.010.18481450.17292788X-RAY DIFFRACTION100
2.01-2.130.18311200.16982837X-RAY DIFFRACTION100
2.13-2.30.18721500.16672785X-RAY DIFFRACTION100
2.3-2.530.19861670.17182781X-RAY DIFFRACTION100
2.53-2.890.16471310.17652830X-RAY DIFFRACTION100
2.89-3.640.16921230.16872855X-RAY DIFFRACTION100
3.64-54.690.15761400.16192891X-RAY DIFFRACTION99.97

+
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://pdbjlvh1.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