[English] 日本語
Yorodumi
- PDB-1rvh: SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rvh
TitleSOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC
Components5'-D(*GP*CP*AP*AP*AP*AP*TP*TP*TP*TP*GP*C)-3'
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, for details see (Padrta et al. (2002) J. Biomol. NMR 24, 1-24)
AuthorsStefl, R. / Wu, H. / Ravindranathan, S. / Sklenar, V. / Feigon, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum.
Authors: Stefl, R. / Wu, H. / Ravindranathan, S. / Sklenar, V. / Feigon, J.
History
DepositionDec 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
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: 5'-D(*GP*CP*AP*AP*AP*AP*TP*TP*TP*TP*GP*C)-3'
B: 5'-D(*GP*CP*AP*AP*AP*AP*TP*TP*TP*TP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3232
Polymers7,3232
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)9 / 30structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 13C-separated NOESY
131DQF-COSY
14231P spin-echo diff CT-HSQC
152spin-echo diff CH-(H)CCH
161HSQC (with and without Pf1 phage)
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING RESIDUAL DIPOLAR COUPLINGS

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM (in duplex)GCAAAATTTTGC, 25mM NH4Cl, 100% D2O or 90% H2O/10% D2Oeither 100% D2O or 90% H2O/10% D2O
22mM (in duplex) GCAAAATTTTGC U-13C,15N, 25mM NH4Cl, 100% D2O100% D2O
Sample conditionsIonic strength: 25 mM NH4Cl / pH: 6 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR softwareName: Amber / Version: 7 / Developer: CASE, D.A., et al. / Classification: refinement
RefinementMethod: simulated annealing, for details see (Padrta et al. (2002) J. Biomol. NMR 24, 1-24)
Software ordinal: 1
Details: the structures are based on a total of 870 restraints, 586 are NOE-derived distance restraints, 160 torsion angle restraints, 24 pseudorotation phase angle restraints, 24 distance restraints ...Details: the structures are based on a total of 870 restraints, 586 are NOE-derived distance restraints, 160 torsion angle restraints, 24 pseudorotation phase angle restraints, 24 distance restraints from W-C hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 9

+
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