[English] 日本語
Yorodumi
- PDB-7bfs: deoxyxylose nucleic acid hairpin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bfs
Titledeoxyxylose nucleic acid hairpin
ComponentsDNA (5'-D(*AP*GP*CP*AP*AP*TP*CP*CP*(XC)P*(XC)P*(XC)P*(XC)P*GP*GP*AP*TP*TP*GP*CP*T)-3')
KeywordsDNA / deoxyxylose nucleic acid / chimeric
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsMattelaer, C.-A. / Mohitosh, M. / Smets, L. / Maiti, M. / Schepers, G. / Mattelaer, H.-P. / Rosemeyer, H. / Herdewijn, P. / Lescrinier, E.
Funding support Belgium, 2items
OrganizationGrant numberCountry
KU LeuvenC14/29/102 Belgium
Research Foundation - Flanders (FWO)1S23217N Belgium
CitationJournal: Chembiochem / Year: 2021
Title: Stable Hairpin Structures Formed by Xylose-Based Nucleic Acids.
Authors: Mattelaer, C.A. / Maiti, M. / Smets, L. / Maiti, M. / Schepers, G. / Mattelaer, H.P. / Rosemeyer, H. / Herdewijn, P. / Lescrinier, E.
History
DepositionJan 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*CP*AP*AP*TP*CP*CP*(XC)P*(XC)P*(XC)P*(XC)P*GP*GP*AP*TP*TP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)6,0631
Polymers6,0631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3910 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: DNA chain DNA (5'-D(*AP*GP*CP*AP*AP*TP*CP*CP*(XC)P*(XC)P*(XC)P*(XC)P*GP*GP*AP*TP*TP*GP*CP*T)-3')


Mass: 6062.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cruciform ColE1 / Source: (synth.) Escherichia coli (E. coli)
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: anisotropic / Type: 2D NOESY

-
Sample preparation

DetailsType: solution / Contents: 2.9 mM oligomer, 100% D2O / Label: D2O / Solvent system: 100% D2O
SampleConc.: 2.9 mM / Component: oligomer / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 M / Label: 1 / pH: 6.6 pD / Pressure: 1 atm / Temperature: 283 K

-
NMR measurement

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

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: explicit solvent
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / 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