[English] 日本語
Yorodumi
- PDB-2lbj: Glycyl-tRNA(GCC) anticodon stem-loop from Bacillus subtilis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lbj
TitleGlycyl-tRNA(GCC) anticodon stem-loop from Bacillus subtilis
ComponentsRNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3')
KeywordsRNA / anticodon stem-loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsChang, A.T. / Nikonowicz, E.P.
CitationJournal: Biochemistry / Year: 2012
Title: Solution Nuclear Magnetic Resonance Analyses of the Anticodon Arms of Proteinogenic and Nonproteinogenic tRNA(Gly).
Authors: Chang, A.T. / Nikonowicz, E.P.
History
DepositionMar 31, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 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: RNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,4341
Polymers5,4341
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)8 / 50structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

-
Components

#1: RNA chain RNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3')


Mass: 5434.277 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D 1H-1H COSY
1322D 1H-1H NOESY
1413D 1H-13C NOESY
1513D (H)CCH-TOCSY
1612D HCN

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.02-0.04 mM [U-98% 13C; U-98% 15N] RNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3'), 100% D2O100% D2O
20.02-0.04 mM RNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3'), 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3')-1[U-98% 13C; U-98% 15N]0.02-0.041
mMRNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3')-20.02-0.042
Sample conditionsIonic strength: 10 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.processing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 8

+
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