[English] 日本語
Yorodumi
- PDB-1at4: INTRAMOLECULAR DNA TRIPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1at4
TitleINTRAMOLECULAR DNA TRIPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GAGAGA-X-TCTCCT-X-CTCTCT), NMR, 7 STRUCTURES
ComponentsDNA (5'-D(*GP*AP*GP*AP*GP*AP*DOP*TP*CP*TP*CP*TP*CP*DOP*CP*TP*CP*TP*CP*T)-3')
KeywordsDNA / INTRAMOLECULAR TRIPLEX / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsBartley, J.P.
CitationJournal: Biochemistry / Year: 1997
Title: Solution conformation of an intramolecular DNA triplex containing a nonnucleotide linker: comparison with the DNA duplex.
Authors: Bartley, J.P. / Brown, T. / Lane, A.N.
History
DepositionAug 18, 1997Processing site: BNL
Revision 1.0Feb 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 23, 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: DNA (5'-D(*GP*AP*GP*AP*GP*AP*DOP*TP*CP*TP*CP*TP*CP*DOP*CP*TP*CP*TP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)5,4431
Polymers5,4431
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)7 / 7LEAST RESTRAINT VIOLATION
Representative

-
Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*AP*GP*AP*DOP*TP*CP*TP*CP*TP*CP*DOP*CP*TP*CP*TP*CP*T)-3')


Mass: 5442.527 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DI-(OCTYLPHOSPHATE) LINKER BETWEEN STRANDS 1 AND 2 AND BETWEEN STRANDS 2 AND 3.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY

-
Sample preparation

Sample conditionspH: 5.0 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

-
Processing

Software
NameClassification
VNMRmodel building
AMBERrefinement
VNMRphasing
NMR software
NameDeveloperClassification
DiscoverMSIrefinement
VNMRstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: RESTRAINED MOLECULAR DYNAMICS USING AMBER FORCEFIELD UNTIL RESIDUAL RESTRAINT ENERGY WAS LESS THAN 1 KCAL MOL-1. THE BEST 12 STRUCTURES HAD PAIRWISE RMSD OF 0.51 A. INSIGHT ALSO WAS USED.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 7 / Conformers submitted total number: 7

+
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