[English] 日本語
Yorodumi
- PDB-2llj: Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2llj
TitleStructure of a bis-naphthalene bound to a thymine-thymine DNA mismatch
Components
  • DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3')
KeywordsDNA / DNA thymine mismatch / macrocyle / bisintercalation
Function / homologyChem-LLJ / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsJourdan, M. / Granzhan, A. / Guillot, R. / Dumy, P. / Teulade-Fichou, M.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch.
Authors: Jourdan, M. / Granzhan, A. / Guillot, R. / Dumy, P. / Teulade-Fichou, M.P.
History
DepositionNov 10, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,2163
Polymers6,6992
Non-polymers5171
Water91951
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 chain DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3')


Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3')


Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-LLJ / 6,22-dioxa-3,9,19,25-tetraazoniapentacyclo[25.5.3.3~11,17~.0~14,37~.0~30,34~]octatriaconta-1(33),11(38),12,14(37),15,17(36),27,29,31,34-decaene / 2,8,19,25-tetraaza-5,22-dioxa-[9,9](2,7)naphthalenophane


Mass: 516.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H44N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY

-
Sample preparation

DetailsContents: 1.5 mM DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3'), 1.5 mM DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3'), 1.5 mM 2,7-bisnaphthalene, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMDNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3')-11
1.5 mMDNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3')-21
1.5 mM2,7-bisnaphthalene-31
Sample conditionsIonic strength: 0.06 / pH: 6 / Pressure: ambient / Temperature: 283 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityPlusVarianUNITYPLUS5001
Varian UnityVarianUNITY8002

-
Processing

NMR software
NameVersionDeveloperClassification
Amber10.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
Amber10.1Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing, molecular 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: 5

+
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://pdbjlvh1.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