[English] 日本語
Yorodumi
- PDB-1bz3: STABILIZATION OF THE ANTICODON STEM-LOOP OF TRNALYS,3 BY AN A+C B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bz3
TitleSTABILIZATION OF THE ANTICODON STEM-LOOP OF TRNALYS,3 BY AN A+C BASE PAIR AND BY PSEUDOURIDINE, NMR, 1 STRUCTURE
ComponentsTRNA
KeywordsRNA / TRNA / PSEUDOURIDINE / ANTICODON
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsDurant, P.C. / Davis, D.R.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine.
Authors: Durant, P.C. / Davis, D.R.
History
DepositionNov 5, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
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: TRNA


Theoretical massNumber of molelcules
Total (without water)5,3501
Polymers5,3501
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 / 60LEAST RESTRAINT VIOLATION
Representative

-
Components

#1: RNA chain TRNA


Mass: 5350.189 Da / Num. of mol.: 1 / Fragment: ANTICODON (RESIDUES 27-43) / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121ROESY
131TOCSY
141HMQC
1511H-31P COSY
1611H-31P HETERO-TOCSY-TOCSY
171DQCOSY
NMR detailsText: LOWEST RMSD DIFFERENCE FROM AVERAGE STRUCTURE. STRUCTURE WAS DETERMINED USING RESTRAINTS FROM HOMONUCLEAR ROESY, DQCOSY AND NOESY DATA. ASSIGNMENTS WERE MADE WITH A COMBINATION OF ROESY, NOESY, ...Text: LOWEST RMSD DIFFERENCE FROM AVERAGE STRUCTURE. STRUCTURE WAS DETERMINED USING RESTRAINTS FROM HOMONUCLEAR ROESY, DQCOSY AND NOESY DATA. ASSIGNMENTS WERE MADE WITH A COMBINATION OF ROESY, NOESY, TOCSY, 1H-13C HMQC AND 1H-31P.

-
Sample preparation

DetailsContents: H2O/D2O
Sample conditionsIonic strength: 100 mM NACL / pH: 5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITY 500 / Manufacturer: Varian / Model: UNITY 500 / Field strength: 500 MHz

-
Processing

Software
NameClassification
VNMRmodel building
AMBERrefinement
VNMRphasing
NMR software
NameVersionDeveloperClassification
Discover95MSIrefinement
VNMRstructure solution
Felixstructure solution
Discoverstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: AMBER FORCEFIELD
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 60 / 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