[English] 日本語
Yorodumi
- PDB-2tpk: AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2tpk
TitleAN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS
ComponentsRNA (MRNA PSEUDOKNOT)
KeywordsRNA / PSEUDOKNOT / T2 / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY-SIMULATED ANNEALING, ENERGY MINIZATION PROTOCOLS
AuthorsHolland, J.A. / Hansen, M.R. / Du, Z. / Hoffman, D.W.
Citation
Journal: Rna / Year: 1999
Title: An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2.
Authors: Holland, J.A. / Hansen, M.R. / Du, Z. / Hoffman, D.W.
#1: Journal: Nucleic Acids Res. / Year: 1997
Title: An NMR and Mutational Study of the Pseudoknot within the Gene 32 Mrna of Bacteriophage T2: Insights Into a Family of Structurally Related RNA Pseudoknots
Authors: Du, Z. / Hoffman, D.W.
History
DepositionOct 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Dec 27, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (MRNA PSEUDOKNOT)


Theoretical massNumber of molelcules
Total (without water)11,5101
Polymers11,5101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 19
Representative

-
Components

#1: RNA chain RNA (MRNA PSEUDOKNOT)


Mass: 11509.891 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA WAS CHEMICALLY SYNTHESIZED FROM GENE 32 OF BACTERIOPHAGE T2.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQFCOSY
131TOCSY
141NOESY-TOCSY
151CT-HSQC
161(H)CCH-COSY
171NOESY-HMQC
181HMQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING NMR SPECTROSCOPY ON 13C,15N-LABELED AND SELECTIVELY DEUTERATED T2 PSEUDOKNOT SAMPLE

-
Sample preparation

Sample conditionspH: 6.5 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerManufacturer: Varian / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Felixstructure solution
XPLOR3.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY-SIMULATED ANNEALING, ENERGY MINIZATION PROTOCOLS
Software ordinal: 1
Details: REFINEMNET DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformers calculated total number: 19 / Conformers submitted total number: 1

+
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