[English] 日本語
Yorodumi
- PDB-2mci: NMR structure of DNA duplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mci
TitleNMR structure of DNA duplex
Components
  • DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')
  • DNA_(5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')
KeywordsDNA / Nucleic acid / DNA duplex
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsBrzezinska, J. / Gdaniec, Z. / Popenda, L. / Markiewicz, W.T.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Polyaminooligonucleotide: NMR structure of duplex DNA containing a nucleoside with spermine residue, N-[4,9,13-triazatridecan-1-yl]-2'-deoxycytidine.
Authors: Brzezinska, J. / Gdaniec, Z. / Popenda, L. / Markiewicz, W.T.
History
DepositionAug 20, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 2458.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized using phosphoramidite chemistry
#2: DNA chain DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')


Mass: 2396.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized using phosphoramidite chemistry

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H COSY
1312D 1H-1H TOCSY
1412D 1H-13C HSQC
1512D 1H-31P HSQC
2622D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3'), 0.5 mM DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3'), 100 % [U-100% 2H] D2O, 50 mM sodium chloride, 10 mM sodium phosphate, 0.1 mM EDTA, 100% D2O100% D2O
20.5 mM DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3'), 0.5 mM DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3'), 10 % [U-100% 2H] D2O, 90 % H2O, 50 mM sodium chloride, 10 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')-11
0.5 mMDNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')-21
100 %D2O-3[U-100% 2H]1
50 mMsodium chloride-41
10 mMsodium phosphate-51
0.1 mMEDTA-61
0.5 mMDNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')-72
0.5 mMDNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')-82
10 %D2O-9[U-100% 2H]2
90 %H2O-102
50 mMsodium chloride-112
10 mMsodium phosphate-122
0.1 mMEDTA-132
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1607ambient atm298 K
2607ambient atm283 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHv2.22Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHv2.22Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpinv2.0Bruker Biospincollection
TopSpinv2.0Bruker Biospinprocessing
Felixv2002Accelrys Software Inc.chemical shift assignment
Felixv2002Accelrys Software Inc.data analysis
Felixv2002Accelrys Software Inc.peak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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