[English] 日本語
Yorodumi
- PDB-1sy8: Structure of DNA sequence d-TGATCA by two-dimensional nuclear mag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sy8
TitleStructure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spec and restrained molecular dynamics
Components5'-D(P*TP*GP*AP*TP*CP*A)-3'
KeywordsDNA / TpG/CpA BASEPAIR STEP / 2D-NMR OF d-TGATCA / RESTRAINED MOLECULAR DYNAMICS / SEQUENCE RELATED CONFORMATION / DNA FLEXIBILITY
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / Simulated annealing, molecular dynamics
AuthorsBarthwal, R. / Awasthi, P. / Narang, M. / Sharma, U. / Srivastava, N.
CitationJournal: J.STRUCT.BIOL. / Year: 2004
Title: Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics
Authors: Barthwal, R. / Awasthi, P. / Narang, M. / Kaur, M. / Sharma, U. / Srivastava, N. / Barthwal, S.K. / Govil, G.
History
DepositionApr 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4May 1, 2024Group: 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: 5'-D(P*TP*GP*AP*TP*CP*A)-3'
B: 5'-D(P*TP*GP*AP*TP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)3,6162
Polymers3,6162
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 / 25structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

-
Components

#1: DNA chain 5'-D(P*TP*GP*AP*TP*CP*A)-3'


Mass: 1808.229 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
122DQF-COSY
NMR detailsText: For imino protons 1D water spectra Vs temperature was also done

-
Sample preparation

Details
Solution-IDContentsSolvent system
13.68mM duplex concentration; 20mM phosphate buffer with 15mM NaClD2O
24.57mM duplex concentration; 20mM phosphate buffer with 15mM NaCl90% H2O/10% D2O
Sample conditionsIonic strength: 20mM Phosphate buffer; 15mM NaCl / pH: 7 / Pressure: AMBIENT / Temperature: 295 K

-
NMR measurement

NMR spectrometerType: Bruker AM / Manufacturer: Bruker / Model: AM / Field strength: 500 MHz

-
Processing

NMR softwareName: Discover / Version: 97 / Classification: refinement
RefinementMethod: Simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structure is based on total 95 intra residue and 26 inter residue NOESY restraints and 12 torsinal angle restraints.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 25 / 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