[English] 日本語
Yorodumi
- PDB-2lps: Molecular dynamics re-refinement of domain 5 of the yeast ai5(gam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lps
TitleMolecular dynamics re-refinement of domain 5 of the yeast ai5(gamma) group II intron
ComponentsRNA (34-MER)
KeywordsRNA / Tetraloop / Bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsHenriksen, N.M. / Davis, D.R. / Cheatham III, T.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.
Authors: Sigel, R.K. / Sashital, D.G. / Abramovitz, D.L. / Palmer, A.G. / Butcher, S.E. / Pyle, A.M.
History
DepositionFeb 17, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 0 THIS ENTRY 2LPS REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (1R2P.MR) ... THIS ENTRY 2LPS REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (1R2P.MR) DETERMINED BY AUTHORS OF THE PDB ENTRY 1R2P: R.K.O.SIGEL,D.G.SASHITAL,D.L.ABRAMOVITZ,A.G.PALMER III, S.E.BUTCHER,A.M.PYLE

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (34-MER)


Theoretical massNumber of molelcules
Total (without water)10,9711
Polymers10,9711
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)5 / 5all calculated structures submitted
RepresentativeModel #1closest to the average

-
Components

#1: RNA chain RNA (34-MER)


Mass: 10970.567 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: This is a Molecular Dynamics re-refinement of structures from the PDB: 1R2P ensemble using the NMR restraints. The re-refinement shows significant changes in the overall geometry
NMR detailsText: AUTHOR USED THE MR DATA FROM ENTRY 1R2P.

-
Processing

NMR softwareName: Amber / Version: 11
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 5 / Conformers submitted total number: 5

+
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