[English] 日本語
Yorodumi
- PDB-2bq2: Solution Structure of the DNA Duplex ACGCGU-NA with a 2' Amido-Li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bq2
TitleSolution Structure of the DNA Duplex ACGCGU-NA with a 2' Amido-Linked Nalidixic Acid Residue at the 3' Terminal Nucleotide
Components5'-D(*AP*CP*GP*CP*GP*2AU)-3'
KeywordsDNA / NUCLEIC ACID / DEOXYRIBONUCLEIC ACID / DISRUPTED TERMINAL BASEPAIRS / QUINOLONE / SYNTHETIC HYBRID / DNA COMPLEX
Function / homologyNALIDIXIC ACID / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsSiegmund, K. / Maheshwary, S. / Narayanan, S. / Connors, W. / Richert, M.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it.
Authors: Siegmund, K. / Maheshwary, S. / Narayanan, S. / Connors, W. / Riedrich, M. / Printz, M. / Richert, C.
History
DepositionApr 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0May 9, 2018Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nmr_spectrometer
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nmr_spectrometer.model
Revision 2.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _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: 5'-D(*AP*CP*GP*CP*GP*2AU)-3'
B: 5'-D(*AP*CP*GP*CP*GP*2AU)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0854
Polymers3,6202
Non-polymers4642
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 80LOWEST CALCULATED ENERGIES
Representative

-
Components

#1: DNA chain 5'-D(*AP*CP*GP*CP*GP*2AU)-3'


Mass: 1810.206 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: NALIDIXIC ACID APPENDED TO THE AMINO FUNCTION OF 2'-AMINOURIDINE VIA AN AMIDE BOND
#2: Chemical ChemComp-NIX / NALIDIXIC ACID


Mass: 232.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O3 / Comment: antibiotic*YM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HSQC
NMR detailsText: NONE

-
Sample preparation

DetailsContents: D2O AND 90% WATER/ 10%D2O
Sample conditionsIonic strength: 160 mM / pH: 7 / Pressure: 1.0 atm / Temperature: 283.0 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SEE PRIMARY CITATION FOR DETAILS
NMR ensembleConformer selection criteria: LOWEST CALCULATED ENERGIES / Conformers calculated total number: 80 / Conformers submitted total number: 2

+
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