[English] 日本語
Yorodumi
- PDB-2jtm: Solution structure of Sso6901 from Sulfolobus solfataricus P2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jtm
TitleSolution structure of Sso6901 from Sulfolobus solfataricus P2
ComponentsPutative uncharacterized protein
KeywordsDNA BINDING PROTEIN / SH3-like
Function / homology
Function and homology information


double-stranded DNA binding / cytoplasm
Similarity search - Function
Chromatin protein Cren7 / Double-stranded DNA-binding Cren7 / Cren7 superfamily / Chromatin protein Cren7 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Chromatin protein Cren7
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsFeng, Y. / Guo, L. / Huang, L. / Wang, J.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea
Authors: Guo, L. / Feng, Y. / Zhang, Z. / Yao, H. / Luo, Y. / Wang, J. / Huang, L.
History
DepositionAug 3, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)6,6781
Polymers6,6781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Putative uncharacterized protein / Sso6901


Mass: 6677.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZE3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY
1422D 1H-15N HSQC
1522D 1H-13C HSQC
1623D CBCA(CO)NH
1723D HN(CA)CB
1823D HBHA(CO)NH
1923D HNCO
11023D HN(CA)CO
11123D 1H-15N TOCSY
11223D (H)CCH-COSY
11323D CCH-TOCSY
11423D 1H-15N NOESY
11523D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0-2.0mM Sso6901, 0.01 % DSS, 50mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
21.0-2.0mM [U-13C; U-15N] Sso6901, 0.01 % DSS, 50mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMSso69011
0.01 %DSS1
50 mMpotassium phosphate1
1.0 mMSso6901[U-13C; U-15N]2
0.01 %DSS2
50 mMpotassium phosphate2
Sample conditionsIonic strength: 0.05 / pH: 6 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.peak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics, simulated annealing / 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