[English] 日本語
Yorodumi
- PDB-2kg7: Structure and features of the complex formed by the tuberculosis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kg7
TitleStructure and features of the complex formed by the tuberculosis virulence factors Rv0287 and Rv0288
Components
  • ESAT-6-like protein esxH
  • Uncharacterized protein esxG (PE family protein)
KeywordsUNKNOWN FUNCTION / Protein complex
Function / homology
Function and homology information


Inhibition of membrane repair / phagocytic vesicle lumen / : / Prevention of phagosomal-lysosomal fusion / extracellular region / metal ion binding / cytosol
Similarity search - Function
ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ESAT-6-like protein EsxG / ESAT-6-like protein EsxH / ESAT-6-like protein EsxH
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 28
AuthorsIlghari, D. / Kirsty, L.L. / Waters, L.C. / Veverka, V.L. / Philip, R.S. / Carr, M.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Solution structure of the M. tuberculosis EsxG-EsxH complex: functional implications and comparisons with other M. tuberculosis Esx family complexes
Authors: Ilghari, D. / Lightbody, K.L. / Veverka, V. / Waters, L.C. / Muskett, F.W. / Renshaw, P.S. / Carr, M.
History
DepositionMar 6, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein esxG (PE family protein)
B: ESAT-6-like protein esxH


Theoretical massNumber of molelcules
Total (without water)20,2702
Polymers20,2702
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)30 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein Uncharacterized protein esxG (PE family protein)


Mass: 9785.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxG, MT0300, Rv0287 / Plasmid: pLeics-01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53692
#2: Protein ESAT-6-like protein esxH / 10 kDa antigen CFP7 / CFP-7 / Low molecular weight protein antigen 7 / Protein TB10.4


Mass: 10483.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxH, cfp7, Rv0288, MT0301, MTV035.16 / Plasmid: pLeics-01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A568, UniProt: P9WNK3*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1372D 1H-1H TOCSY
1472D 1H-1H NOESY
1513D 1H-15N NOESY
1613D 1H-15N TOCSY
1733D (H)CCH-TOCSY
1833D 1H-13C NOESY
1953D HNCA
11053D HN(CA)CB
11153D CBCA(CO)NH
1125TROSY HN(CO)CA
11322D 1H-15N HSQC
11442D 1H-13C HSQC
11523D 1H-15N NOESY
11623D 1H-15N TOCSY
11743D (H)CCH-COSY
11843D 1H-13C NOESY
11963D HNCA
12063D HN(CA)CB
12163D CBCA(CO)NH
1226TROSY HN(CO)CA

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1mM [U-98% 15N] Labelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-1, 90% H2O/10% D2O90% H2O/10% D2O
20.7-1mM [U-98% 15N] Labelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-2, 90% H2O/10% D2O90% H2O/10% D2O
30.7-1mM [U-99% 13C] Labelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-3, 100% D2O100% D2O
40.7-1mM [U-99% 13C] Labelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-4, 100% D2O100% D2O
50.7-1mM [U-99% 13C; U-98% 15N] Labelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-5, 90% H2O/10% D2O90% H2O/10% D2O
60.7-1mM [U-99% 13C; U-98% 15N] Labelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-6, 90% H2O/10% D2O90% H2O/10% D2O
70.7-1mM Unlabelled Unlabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-7, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMLabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-1[U-98% 15N]0.7-11
mMLabelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-2[U-98% 15N]0.7-12
mMLabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-3[U-99% 13C]0.7-13
mMLabelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-4[U-99% 13C]0.7-14
mMLabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-5[U-99% 13C; U-98% 15N]0.7-15
mMLabelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-6[U-99% 13C; U-98% 15N]0.7-16
mMUnlabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-7Unlabelled0.7-17
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker DRXBrukerDRX6003

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Topspin 2.0Bruker Biospincollection
TopSpinBruker Topspin 2.0Bruker Biospinprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
ProcheckNMRLaskowski, MacArthurdata analysis
CYANAGuntert, Mumenthaler, Wuthrichstructure solution
CYANAGuntert, Mumenthaler, Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 30

+
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