[English] 日本語
Yorodumi
- PDB-1ajl: FIVE-NUCLEOTIDE BULGE LOOP FROM TETRAHYMENA THERMOPHILA GROUP I INTRON -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ajl
TitleFIVE-NUCLEOTIDE BULGE LOOP FROM TETRAHYMENA THERMOPHILA GROUP I INTRON
Components
  • RNA (5'-R(*GP*AP*GP*UP*AP*CP*C)-3')
  • RNA (5'-R(*GP*GP*UP*AP*AP*UP*AP*AP*GP*CP*UP*C)-3')
KeywordsRNA / RNA BULGE LOOP / GROUP I INTRON / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsLuebke, K.J. / Landry, S.M. / Tinoco Junior, I.
CitationJournal: Biochemistry / Year: 1997
Title: Solution conformation of a five-nucleotide RNA bulge loop from a group I intron.
Authors: Luebke, K.J. / Landry, S.M. / Tinoco, I.
History
DepositionMay 6, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*UP*AP*AP*UP*AP*AP*GP*CP*UP*C)-3')
B: RNA (5'-R(*GP*AP*GP*UP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0572
Polymers6,0572
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)1 / 20LEAST RESTRAINT VIOLATION
Representative

-
Components

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


Mass: 3836.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FIVE-NUCLEOTIDE BULGE / Source: (gene. exp.) Tetrahymena thermophila (eukaryote)
Description: IN VITRO TRANSCRIPT FROM OLIGONUCLEOTIDE TEMPLATE USING T7 RNA POLYMERASE
#2: RNA chain RNA (5'-R(*GP*AP*GP*UP*AP*CP*C)-3')


Mass: 2220.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FIVE-NUCLEOTIDE BULGE / Source: (gene. exp.) Tetrahymena thermophila (eukaryote)
Description: IN VITRO TRANSCRIPT FROM OLIGONUCLEOTIDE TEMPLATE USING T7 RNA POLYMERASE

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131HMQC
141TOCSY
151TOCSY-NOESY
161H-P CORRELATED

-
Sample preparation

Sample conditionspH: 6.7 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX300BrukerAMX3003001
Bruker AMX600BrukerAMX6006002
GE GN500GEGN5005003

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLOR2.2BRUNGERrefinement
FELIX230structure solution
X-PLOR2.2structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 20 / 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