[English] 日本語
Yorodumi
- PDB-2krv: Solution structure of the E. coli tRNA-Arg1 (ICG) ASL containing ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2krv
TitleSolution structure of the E. coli tRNA-Arg1 (ICG) ASL containing the 2-thiocytidine modification
ComponentsRNA (5'-R(*CP*UP*CP*GP*GP*(RSP)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')
KeywordsRNA / tRNA / 2-thiocytidine / modification / ASL
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsBilbille, Y. / Agris, P.F.
CitationJournal: To be Published
Title: Solution structure of the tRNA-Arg-1 (ICG) ASL containg the 2-thiocytidine modification in position 32.
Authors: Bilbille, Y. / Cantara, W.A. / Kim, J. / Agris, P.F.
History
DepositionDec 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _chem_comp.mon_nstd_flag / _database_2.pdbx_DOI ..._chem_comp.mon_nstd_flag / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*CP*UP*CP*GP*GP*(RSP)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,4581
Polymers5,4581
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: RNA chain RNA (5'-R(*CP*UP*CP*GP*GP*(RSP)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')


Mass: 5458.367 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1322D DQF-COSY
1412D 1H-1H COSY
1512D 1H-1H TOCSY
1622D 1H-13C HSQC
1722D 1H-31P HETCOR

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-1, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.8 mMRNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-11
0.8 mMRNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-22
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE5002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
TopSpinBruker Biospincollection
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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