[English] 日本語
Yorodumi
- PDB-1b3p: 5'-D(*GP*GP*AP*GP*GP*AP*T)-3' -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b3p
Title5'-D(*GP*GP*AP*GP*GP*AP*T)-3'
ComponentsDNA (5'-D(*GP*GP*AP*GP*GP*AP*T)-3')
KeywordsDNA / (G-G-A) TRIPLET REPEAT / V-SHAPED BACKBONE / PARALLEL-STRANDED SEGMENTS / MISMATCH ALIGNMENTS / UNIFORM 13C / 15N-LABELED DNA
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / distance geometry
AuthorsKettani, A. / Bouaziz, S. / Skripkin, E. / Majumdar, A. / Wang, W. / Jones, R.A. / Patel, D.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Interlocked mismatch-aligned arrowhead DNA motifs.
Authors: Kettani, A. / Bouaziz, S. / Skripkin, E. / Majumdar, A. / Wang, W. / Jones, R.A. / Patel, D.J.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*AP*GP*GP*AP*T)-3')
B: DNA (5'-D(*GP*GP*AP*GP*GP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)4,4052
Polymers4,4052
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)15 / 100ACCEPTABLE COVALENT GEOMETRY, LOW DISTANCE RESTRAINTS VIIOLATIONS AND FAVORABLE NON-BONDED ENERGY VALUES
Representative

-
Components

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


Mass: 2202.472 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
14113C-EDITED 13C-PURGED NOESY
15115N-EDITED 15N-PURGED NOESY
161HNN-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR AND HETERONUCLEAR EXPERIMENTS ON 13C AND 15N LABELED SAMPLE. THE DISTANCE RESTRAINTS WERE DEDUCED FROM 5 NOESY MIXING TIMES (50, 100, 150, 200 ...Text: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR AND HETERONUCLEAR EXPERIMENTS ON 13C AND 15N LABELED SAMPLE. THE DISTANCE RESTRAINTS WERE DEDUCED FROM 5 NOESY MIXING TIMES (50, 100, 150, 200 AND 250 MS) IN D2O AND 2 NOESY MIXING TIMES IN H2O (60 AND 200 MS) MS

-
Sample preparation

Sample conditionsIonic strength: 10 mM NACL, 2 mM PHOSPHATE / pH: 6.6 / Pressure: ambient / Temperature: 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851BRUNGERstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JNRL CITATION ABOVE
NMR ensembleConformer selection criteria: ACCEPTABLE COVALENT GEOMETRY, LOW DISTANCE RESTRAINTS VIIOLATIONS AND FAVORABLE NON-BONDED ENERGY VALUES
Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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