[English] 日本語
Yorodumi
- PDB-2l7d: Ribonucleotide Perturbation of DNA Structure: Solution Structure ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l7d
TitleRibonucleotide Perturbation of DNA Structure: Solution Structure of [d(CGC)r(G)d(AATTCGCG)]2
Components5'-D(*CP*GP*C)-R(P*G)-D(P*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / RNA / Ribonucleotide substituted DNA
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsDeRose, E.F. / Perera, L. / Murray, M.S. / Kunkel, T.A. / London, R.E.
CitationJournal: Biochemistry / Year: 2012
Title: Solution structure of the Dickerson DNA dodecamer containing a single ribonucleotide.
Authors: DeRose, E.F. / Perera, L. / Murray, M.S. / Kunkel, T.A. / London, R.E.
History
DepositionDec 7, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 13, 2012Group: Database references
Revision 1.3May 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(*CP*GP*C)-R(P*G)-D(P*AP*AP*TP*TP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*C)-R(P*G)-D(P*AP*AP*TP*TP*CP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,3592
Polymers7,3592
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)5 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: DNA/RNA hybrid 5'-D(*CP*GP*C)-R(P*G)-D(P*AP*AP*TP*TP*CP*GP*CP*G)-3'


Mass: 3679.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: rG4 substituted Drew Dickerson dodecamer

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1412D 1H-1H COSY
1522D 1H-1H NOESY
1612D 1H-31P COSY
1712D 1H-31P J-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM rG4 substituted Drew Dickerson dodecamer, 50.0 mM sodium chloride, 50.0 mM sodium phosphate, 0.5 mM EDTA, 100% D2O100% D2O
22.0 mM rG4 substituted Drew Dickerson dodecamer, 50.0 mM sodium chloride, 50.0 mM sodium phosphate, 0.5 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2.0 mMrG4 substituted Drew Dickerson dodecamer-11
50.0 mMsodium chloride-21
50.0 mMsodium phosphate-31
0.5 mMEDTA-41
2.0 mMrG4 substituted Drew Dickerson dodecamer-52
50.0 mMsodium chloride-62
50.0 mMsodium phosphate-72
0.5 mMEDTA-82
2.0 mMrG4 substituted Drew Dickerson dodecamer-93
50.0 mMsodium chloride-103
50.0 mMsodium phosphate-113
0.5 mMEDTA-123
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
NMRPipe2010.190.16.149Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView8.0.b64Johnson, One Moon Scientificchemical shift assignment
NMRView8.0.b64Johnson, One Moon Scientificdata analysis
NMRView8.0.b64Johnson, One Moon Scientificpeak picking
XPLOR-NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
XPLOR-NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 212 / Hydrogen bond constraints total count: 92
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 5
NMR ensemble rmsDistance rms dev: 0.096 Å / Distance rms dev error: 0.02 Å

+
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