[English] 日本語
Yorodumi
- PDB-2dsm: NMR Structure of Bacillus Subtilis Protein YqaI, Northeast Struct... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dsm
TitleNMR Structure of Bacillus Subtilis Protein YqaI, Northeast Structural Genomics Target SR450
ComponentsHypothetical protein yqaI
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / homodimer / domain swapped dimer / inter-domain beta sheet / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYqaI domain / Uncharacterised protein family YqaI / YqaI domain superfamily / Hypothetical protein Yqai / Herpes Virus-1 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YqaI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR
AuthorsRamelot, T.A. / Cort, J.R. / Wang, D. / Janua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. ...Ramelot, T.A. / Cort, J.R. / Wang, D. / Janua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: to be published
Title: NMR Structure of Bacillus Subtilis Protein YqaI, Northeast Structural Genomics Target SR450
Authors: Ramelot, T.A. / Cort, J.R. / Wang, D. / Janua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJul 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein yqaI
B: Hypothetical protein yqaI


Theoretical massNumber of molelcules
Total (without water)17,3072
Polymers17,3072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

-
Components

#1: Protein Hypothetical protein yqaI


Mass: 8653.513 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqaI or BSU26300 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Lamda DE3) pMGK / References: UniProt: P45906

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 13C-separated NOESY
1424D 13C/15N-separated NOESY
153HNHA

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM YqaI, U-15N, 13C; 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 95% D2O, 5% D2O95% D2O, 5% D2O
21.0mM YqaI, U-15N, 13C; 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 100% D2O100% D2O
31.4mM YqaI, U-15N, 5%-13C, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 95% D2O, 5% D2O95% D2O, 5% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameVersionClassification
Sparky3.1data analysis
NMRPipeLinux9processing
X-PLORxplor-nih-2.11.2refinement
CNS1.1refinement
VNMR6.1Ccollection
AutoStructure2.1.1data analysis
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / 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://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