[English] 日本語
Yorodumi
- PDB-1g7z: NMR SOLUTION STRUCTURE OF D(CGCTAGCG)2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g7z
TitleNMR SOLUTION STRUCTURE OF D(CGCTAGCG)2
Components5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3'
KeywordsDNA / TOTO / C13 DYNAMICS / CONFORMATIONAL EXCHANGE / PHOSPHATE CONFORMATION / DEOXYRIBOSE CONFORMATION / HELICAL PARAMETER / ORDER PARAMETER
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / The RANDMARDI procedure of the complete relaxation matrix analysis method, MARDIGRAS, was used to calculate interproton distance bounds from the integrated NOESY cross-peak intensities. These distance bounds were then used as restraints in an RMD procedure to yield 20 structures.
AuthorsIsaacs, R.J. / Spielmann, H.P.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters ...Title: Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters implies conformational coupling in dinucleotide units.
Authors: Isaacs, R.J. / Spielmann, H.P.
#1: Journal: Biochemistry / Year: 1998
Title: Dynamics of a Bis-intercalator DNA Complex by 1H-Detected Natural Abundance 13C NMR Spectroscopy
Authors: Spielmann, H.P.
#2: Journal: Biochemistry / Year: 1995
Title: Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy.
Authors: Spielmann, H.P. / Wemmer, D.E. / Jacobsen, J.P.
History
DepositionNov 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
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(*CP*GP*CP*TP*AP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
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)20 / 20back calculated data agree with experimental NOESY spectrum
RepresentativeModel #12lowest pairwise rmsd from other conformers

-
Components

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


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phosphoramadites on solid support

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

DetailsContents: 4 mM DNA duplex / Solvent system: 99.96% D2O
Sample conditionsIonic strength: NaCl(100mM),PO4-(20mM),NaN3(10mM),EDTA(0.1mM)
pH: 7.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVariancollection
Felix98MSIdata analysis
MARDIGRAS3.2James, TLiterative matrix relaxation
Discover2.98MSIstructure solution
Discover2.98MSIrefinement
RefinementMethod: The RANDMARDI procedure of the complete relaxation matrix analysis method, MARDIGRAS, was used to calculate interproton distance bounds from the integrated NOESY cross-peak intensities. These ...Method: The RANDMARDI procedure of the complete relaxation matrix analysis method, MARDIGRAS, was used to calculate interproton distance bounds from the integrated NOESY cross-peak intensities. These distance bounds were then used as restraints in an RMD procedure to yield 20 structures.
Software ordinal: 1
Details: The structures are based on a total of 540 restraints, 518 are NOE-derived distance constraints and 22 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest pairwise rmsd from other conformers
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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