[English] 日本語
Yorodumi
- PDB-1p83: NMR STRUCTURE OF 1-25 FRAGMENT OF MYCOBACTERIUM TUBERCULOSIS CPN10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p83
TitleNMR STRUCTURE OF 1-25 FRAGMENT OF MYCOBACTERIUM TUBERCULOSIS CPN10
Components10 kDa chaperonin
KeywordsCHAPERONE / Cpn10 / Mycobacterium tuberculosis / Helix formation
Function / homology
Function and homology information


zymogen binding / cell wall / chaperone cofactor-dependent protein refolding / protein folding chaperone / peptidoglycan-based cell wall / unfolded protein binding / cellular response to heat / response to heat / protein-folding chaperone binding / response to antibiotic ...zymogen binding / cell wall / chaperone cofactor-dependent protein refolding / protein folding chaperone / peptidoglycan-based cell wall / unfolded protein binding / cellular response to heat / response to heat / protein-folding chaperone binding / response to antibiotic / regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular region / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / GroES-like superfamily
Similarity search - Domain/homology
Co-chaperonin GroES / Co-chaperonin GroES
Similarity search - Component
MethodSOLUTION NMR / molecular dynamics
AuthorsCiutti, A. / Spiga, O. / Giannozzi, E. / Scarselli, M. / Di Maro, D. / Calamandrei, D. / Niccolai, N. / Bernini, A.
Citation
Journal: To be Published
Title: Solution Structure of 1-25 fragment of Cpn10 from Mycobacterium Tuberculosis
Authors: Ciutti, A. / Spiga, O. / Giannozzi, E. / Scarselli, M. / Di Maro, D. / Calamandrei, D. / Niccolai, N. / Bernini, A.
#1: Journal: To be Published
Title: Mycobacterium tuberculosis chaperonin 10 is secreted in the macrophage phagolysosome: Is secretion due to dissociation and the adoption of partially helical structure at the membrane
Authors: Fossati, G. / Izzo, G. / Rizzi, E. / Gancia, E. / Modena, D. / Moras, M.L. / Niccolai, N. / Giannozzi, E. / Spiga, O. / Bono, L. / Marone, P. / Leone, E. / Mangili, F. / Harding, S. / ...Authors: Fossati, G. / Izzo, G. / Rizzi, E. / Gancia, E. / Modena, D. / Moras, M.L. / Niccolai, N. / Giannozzi, E. / Spiga, O. / Bono, L. / Marone, P. / Leone, E. / Mangili, F. / Harding, S. / Errington, N. / Walter, C. / Henderson, B. / Roberts, M.M. / Coates, A.R.M. / Casetta, B. / Mascagni, P.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 10 kDa chaperonin


Theoretical massNumber of molelcules
Total (without water)2,6871
Polymers2,6871
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)20 / 100structures with the lowest energy
RepresentativeModel #20lowest energy

-
Components

#1: Protein/peptide 10 kDa chaperonin / Protein Cpn10 / groES protein / BCG-A heat shock protein / 10 kDa antigen


Mass: 2687.026 Da / Num. of mol.: 1 / Fragment: N-terminal Domain, residue 1-25 / Source method: obtained synthetically / Details: Solid phase synthesis / References: UniProt: P09621, UniProt: P9WPE5*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

DetailsContents: 2 mM 1-25 fragment of Cpn10 / Solvent system: 50% HFA 45% H2O 5% D2O
Sample conditionsPressure: ambient / Temperature: 300 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker Spectrospincollection
XwinNMR2.1Bruker Spectrospinprocessing
NMRView4.1Bruce Johnsondata analysis
DYANA1.5Guntertstructure solution
Amber5.1Case, Pearlmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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