[English] 日本語
Yorodumi
- PDB-1jve: NMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jve
TitleNMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop
ComponentsAT-Rich DNA with the GAA-Hairpin Loop
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DNA OLIGONUCLEOTIDE / STEM-AND-LOOP / AT-RICH / GAA HAIRPIN LOOP / PRIBNOW BOX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / full matrix relaxation analysis of NOE, random error analysis of NOE, simulated annealing using torsion angle dynamics, simulated annealing using Metropolis Monte Carlo, restrained minimization
AuthorsUlyanov, N.B. / Bauer, W.R. / James, T.L.
CitationJournal: J.Biomol.NMR / Year: 2002
Title: High-resolution NMR structure of an AT-rich DNA sequence.
Authors: Ulyanov, N.B. / Bauer, W.R. / James, T.L.
History
DepositionAug 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2002Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AT-Rich DNA with the GAA-Hairpin Loop


Theoretical massNumber of molelcules
Total (without water)8,3221
Polymers8,3221
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)10 / 50Lowest target function (a weighted sum of conformational energy and restraint energy).
RepresentativeModel #1lowest energy

-
Components

#1: DNA chain AT-Rich DNA with the GAA-Hairpin Loop


Mass: 8322.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Designed AT-rich sequence

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
121DQF-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

DetailsContents: 2mM DNA; phosphate buffer: 30 mM K+; 1mM EDTA / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 30 mM K+ / pH: 8 / Pressure: ambient / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Associates, Inc.collection
NMRPipe1.8Delaglio, F.processing
Sparky3.1Goddard, T.D., Kneller, D.G.data analysis
MARDIGRAS3.2Borgias, B.A., Thomas, P.D., Liu, H., Kumar, A., Tonelli, M.iterative matrix relaxation
DYANA1.5Guntert, P.refinement
miniCarloalpha versionUlyanov, N.B., Gorler, A., Gorin, A.A., Zhurkin, V.B.refinement
RefinementMethod: full matrix relaxation analysis of NOE, random error analysis of NOE, simulated annealing using torsion angle dynamics, simulated annealing using Metropolis Monte Carlo, restrained minimization
Software ordinal: 1
Details: The NMR refinement was based on a total of 434 interproton distance restraints (16.1 per residue). The restraints include 353 MARDIGRAS-derived quantitative restraints for nonexchangeable ...Details: The NMR refinement was based on a total of 434 interproton distance restraints (16.1 per residue). The restraints include 353 MARDIGRAS-derived quantitative restraints for nonexchangeable protons (with an average flat-well width of 1.51 angstroms), 63 qualitative restraints for exchangeable protons, and 18 H-bond restraints for Watson-Crick GC pairs.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Lowest target function (a weighted sum of conformational energy and restraint energy).
Conformers calculated total number: 50 / 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