[English] 日本語
Yorodumi
- PDB-2lqj: Solution structure of the C-terminal domain of the MgtC protein f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lqj
TitleSolution structure of the C-terminal domain of the MgtC protein from Mycobacterium tuberculosis
ComponentsMg2+ transport protein
KeywordsHYDROLASE / tuberculosis / ACT domain / membrane protein / regulation
Function / homology
Function and homology information


cellular response to magnesium starvation / : / membrane => GO:0016020 / plasma membrane
Similarity search - Function
MgtC/SapB/SrpB/YhiD family / MgtC family / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mg2+ transport protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsYang, M. / Yang, Y. / Labesse, G. / Blanc-Potard, A.
CitationJournal: J.Bacteriol. / Year: 2012
Title: The C-Terminal Domain of the Virulence Factor MgtC Is a Divergent ACT Domain.
Authors: Yang, Y. / Labesse, G. / Carrere-Kremer, S. / Esteves, K. / Kremer, L. / Cohen-Gonsaud, M. / Blanc-Potard, A.B.
History
DepositionMar 7, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mg2+ transport protein


Theoretical massNumber of molelcules
Total (without water)10,4151
Polymers10,4151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Mg2+ transport protein / POSSIBLE Mg2+ TRANSPORT P-TYPE ATPASE C MGTC


Mass: 10414.767 Da / Num. of mol.: 1 / Fragment: UNP residues 141-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37rv / Gene: mgtC, MT1859, Rv1811 / Production host: Escherichia coli (E. coli) / References: UniProt: O07221, EC: 3.6.3.1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1423D HNCO
1523D HNCA
1623D CBCA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMentity-1[U-100% 15N]1
0.3 mMentity-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.11 / pH: 4.6 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges, and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1188 / NOE intraresidue total count: 240 / NOE long range total count: 380 / NOE medium range total count: 210 / NOE sequential total count: 358 / Protein chi angle constraints total count: 17 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 69 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 2.209 ° / Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 15 / Maximum lower distance constraint violation: 0.2 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.3 Å / Torsion angle constraint violation method: RECORD SCRIPTS
NMR ensemble rmsDistance rms dev: 0.0178 Å / Distance rms dev error: 0.012 Å

+
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