[English] 日本語
Yorodumi
- PDB-1fv8: NMR STUDY OF AN HETEROCHIRAL HAIRPIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fv8
TitleNMR STUDY OF AN HETEROCHIRAL HAIRPIN
Components5'-D(*TP*AP*TP*CP*AP*(0DT)P*CP*GP*AP*TP*A)-3'
KeywordsDNA / Hairpin / heterochiral loop / flexibilty / antisense DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsEl Amri, C. / Mauffret, O. / Santamaria, F. / Rayner, B. / Fermandjian, S.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2001
Title: NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop.
Authors: El Amri, C. / Mauffret, O. / Santamariar, F. / Tevanian, G. / Rayner, B. / Fermandjian, S.
History
DepositionSep 19, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*TP*AP*TP*CP*AP*(0DT)P*CP*GP*AP*TP*A)-3'


Theoretical massNumber of molelcules
Total (without water)3,3321
Polymers3,3321
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)11 / 50structures with the lowest energy
RepresentativeModel #11closest to the average,minimized average structure

-
Components

#1: DNA chain 5'-D(*TP*AP*TP*CP*AP*(0DT)P*CP*GP*AP*TP*A)-3'


Mass: 3332.210 Da / Num. of mol.: 1 / Fragment: AT(L)C HAIRPIN / Source method: obtained synthetically
Details: This sequence comes from a pBR322 topoisomerase II cleavage site

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121P-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques, and PFG to measure the diffusion constant

-
Sample preparation

Details
Solution-IDContentsSolvent system
1AT(L)C90% H2O/10% D2O
2AT(L)C100% D2O
Sample conditionsIonic strength: 0.025 / pH: 6 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
FelixMSI (SAn Diego)data analysis
CNSXPLOR 3.8Brunger et al., 1998structure solution
XwinNMRBrukerprocessing
CNSXPLOR 3.8Brunger et al., 1998refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 252 restraints, distance constraints, 56 dihedral angle restraints,9 distance restraints from hydrogen bonds, and 4 planarity constraints. The ...Details: The structures are based on a total of 252 restraints, distance constraints, 56 dihedral angle restraints,9 distance restraints from hydrogen bonds, and 4 planarity constraints. The calculations were performed on the 11 central residues.
NMR representativeSelection criteria: closest to the average,minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 11

+
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