[English] 日本語
Yorodumi
- PDB-2lyg: Fuc_TBA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lyg
TitleFuc_TBA
ComponentsDNA (5'-D(P*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
KeywordsDNA / Carbohydrate-DNA interaction / G-Quadruplex structure
Function / homology2-hydroxyethyl 6-deoxy-beta-L-galactopyranoside / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsGomez-Pinto, I. / Vengut-Climent, E. / Lucas, R. / Avio, A. / Eritja, R. / Gonzalez-Ibaez, C. / Morales, J.
CitationJournal: Chemistry / Year: 2013
Title: Carbohydrate-DNA interactions at G-quadruplexes: folding and stability changes by attaching sugars at the 5'-end.
Authors: Gomez-Pinto, I. / Vengut-Climent, E. / Lucas, R. / Avino, A. / Eritja, R. / Gonzalez, C. / Morales, J.C.
History
DepositionSep 18, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(P*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9512
Polymers4,7431
Non-polymers2081
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 12structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Sugar ChemComp-1CF / 2-hydroxyethyl 6-deoxy-beta-L-galactopyranoside / 2-hydroxyethyl 6-deoxy-beta-L-galactoside / 2-hydroxyethyl 6-deoxy-L-galactoside / 2-hydroxyethyl 6-deoxy-galactoside


Type: L-saccharide / Mass: 208.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1412D 1H-1H COSY
NMR detailsText: The structure was determined using NOE data

-
Sample preparation

DetailsContents: 1 mM DNA (5'-D(P*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'), 1 mM SUGAR (ALPHA-D-FUCOSE), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDNA (5'-D(P*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')-11
1 mMSUGAR (ALPHA-D-FUCOSE)-21
Sample conditionspH: 7 / Pressure: ambient / Temperature: 279.6 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 12 / Conformers submitted total number: 12

+
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