[English] 日本語
Yorodumi
- PDB-2li4: Solution structure of a shortened antiterminator hairpin from a M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2li4
TitleSolution structure of a shortened antiterminator hairpin from a Mg2+ riboswitch
ComponentsRNA (32-MER)
KeywordsRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKorth, M.M.T. / Sigel, R.K.O.
CitationJournal: To be Published
Title: Solution structure of a shortened antiterminator hairpin from a Mg2+ riboswitch
Authors: Korth, M.M.T. / Sigel, R.K.O.
History
DepositionAug 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 22, 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 / pdbx_nmr_spectrometer
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (32-MER)


Theoretical massNumber of molelcules
Total (without water)10,3041
Polymers10,3041
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain RNA (32-MER)


Mass: 10304.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Yersinia enterocolitica (bacteria)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
1332D 1H-1H NOESY
3442D 1H-1H TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
150 mM potassium chloride, 10 uM EDTA, 0.24 mM RNA (32-MER), 100% D2O100% D2O
250 mM potassium chloride, 10 uM EDTA, 0.6 mM RNA (32-MER), 90% H2O/10% D2O90% H2O/10% D2O
350 mM potassium chloride, 10 uM EDTA, 0.8 mM RNA (32-MER), 100% D2O100% D2O
450 mM potassium chloride, 10 uM EDTA, 0.5 mM RNA (32-MER), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMpotassium chloride-11
10 uMEDTA-21
0.24 mMRNA (32-MER)-31
50 mMpotassium chloride-42
10 uMEDTA-52
0.6 mMRNA (32-MER)-62
50 mMpotassium chloride-73
10 uMEDTA-83
0.8 mMRNA (32-MER)-93
50 mMpotassium chloride-104
10 uMEDTA-114
0.5 mMRNA (32-MER)-124
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.056.8ambient 303 K
20.056.8ambient 278 K
30.056.8ambient 293 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
TopSpin1.3, 2.1, 3.0aBruker Biospinprocessing
X-PLOR2.24Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR2.24Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 569
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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