[English] 日本語
Yorodumi
- PDB-1zyg: Structure of a Supercoiling Responsive DNA Site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zyg
TitleStructure of a Supercoiling Responsive DNA Site
Components5'-D(*CP*AP*AP*CP*CP*CP*GP*GP*GP*TP*TP*G)-3'
KeywordsDNA / supercoiling / Hix / recombinase / Hin
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion anlge dynamics
Model type detailsminimized average
AuthorsBae, S.H. / Yun, S.H. / Sun, D. / Lim, H.M. / Choi, B.S.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structural and dynamic basis of a supercoiling-responsive DNA element
Authors: Bae, S.H. / Yun, S.H. / Sun, D. / Lim, H.M. / Choi, B.S.
History
DepositionJun 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*AP*AP*CP*CP*CP*GP*GP*GP*TP*TP*G)-3'
B: 5'-D(*CP*AP*AP*CP*CP*CP*GP*GP*GP*TP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
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)15 / 100structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1minimized average structure

-
Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid-support Phosphoramide Chemistry

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
1422D COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
110mM sodium phosphate (pH 6.8), 100mM NaCl90% H2O/10% D2O
210mM sodium phosphate (pH 6.8), 100mM NaCl100% D2O
Sample conditionsIonic strength: 10mM sodium phosphate, 100mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 295 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR3.1CVarian Inc.collection
NMRPipe1995Bax, A.processing
MARDIGRAS3.2James, T.iterative matrix relaxation
X-PLORXPLOR-NIHClorestructure solution
X-PLORXPLOR-NIHrefinement
RefinementMethod: simulated annealing, torsion anlge dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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