[English] 日本語
Yorodumi
- PDB-149d: SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 149d
TitleSOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES
Components
  • 5'-D(*CP*CP*TP*AP*TP*TP*C)-3'
  • 5'-D(*CP*TP*TP*GP*TP*CP*C)-3'
  • 5'-D(*GP*AP*AP*TP*AP*GP*G)-3'
KeywordsDNA / TRIPLEX
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR
AuthorsRadhakrishnan, I. / Patel, D.J.
Citation
Journal: Structure / Year: 1994
Title: Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples.
Authors: Radhakrishnan, I. / Patel, D.J.
#1: Journal: Biochemistry / Year: 1992
Title: Three-Dimensional Homonuclear Noesy-Tocsy of an Intramolecular Pyrimidine(Dot)Purine(Dot)Pyrimidine DNA Triplex Containing a Central G(Dot)Ta Triple: Nonexchangeable Proton Assignments and Structural Implications
Authors: Radhakrishnan, I. / Patel, D.J. / Gao, X.
#2: Journal: J.Am.Chem.Soc. / Year: 1992
Title: Solution Conformation of a G(Dot)Ta Triple in an Intramolecular Pyrimidine(Dot)Purine(Dot)Pyrimidine DNA Triplex
Authors: Radhakrishnan, I. / Patel, D.J. / Veal, J.M. / Gao, X.
#3: Journal: Biochemistry / Year: 1991
Title: NMR Structural Studies of Intramolecular (Y+)N(Dot)(R+)N(Y-)N DNA Triplexes in Solution: Imino and Amino Proton and Nitrogen Markers of G(Dot)Ta Base Triple Formation
Authors: Radhakrishnan, I. / Gao, X. / De Los Santos, C. / Live, D. / Patel, D.J.
History
DepositionNov 15, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*CP*TP*AP*TP*TP*C)-3'
B: 5'-D(*GP*AP*AP*TP*AP*GP*G)-3'
C: 5'-D(*CP*TP*TP*GP*TP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,2993
Polymers6,2993
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: THREE RESIDUES IN THE SEQUENCE STUDIED ARE CYTOSINES THAT ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES DIFFER FROM "NORMAL" CYTOSINES IN THAT THEY HAVE A PROTON ATTACHED TO THE N3 NITROGEN. ...1: THREE RESIDUES IN THE SEQUENCE STUDIED ARE CYTOSINES THAT ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES DIFFER FROM "NORMAL" CYTOSINES IN THAT THEY HAVE A PROTON ATTACHED TO THE N3 NITROGEN. IT SHOULD BE NOTED THAT THIS IS NOT A PERMANENT MODIFICATION BUT RATHER A CONSEQUENCE OF THE CONDITIONS UNDER WHICH THE SEQUENCE WAS STUDIED. THESE N3-PROTONATED CYTOSINE RESIDUES HAVE BEEN ASSIGNED THE RESIDUE NAME C IN THE ENTRY AND ATOM H3 HAS BEEN FOOTNOTED.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / -
Representative

-
Components

#1: DNA chain 5'-D(*CP*CP*TP*AP*TP*TP*C)-3'


Mass: 2048.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#2: DNA chain 5'-D(*GP*AP*AP*TP*AP*GP*G)-3'


Mass: 2186.473 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*TP*TP*GP*TP*CP*C)-3'


Mass: 2064.372 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: R VALUE 0.022 RMSD BOND DISTANCES 0.005 ANGSTROMS RMSD BOND ANGLES 2.26 DEGREES
NMR ensembleConformers submitted total number: 14

+
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