[English] 日本語
Yorodumi
- PDB-177d: SOLUTION STRUCTURE AND HYDRATION PATTERNS OF A PYRIMIDINE(DOT)PUR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 177d
TitleSOLUTION STRUCTURE AND HYDRATION PATTERNS OF A PYRIMIDINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING A NOVEL T(DOT)CG TRIPLE
ComponentsDNA (5'-D(*GP*AP*AP*CP*AP*GP*GP*TP*TP*TP*TP*T*CP*CP*TP*GP*TP*TP*CP*TP*TP*TP*TP*T*CP*TP*TP*TP*TP*CP*C)-3')
KeywordsDNA / TRIPLEX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, DISTANCE GEOMETRY
AuthorsRadhakrishnan, I. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple.
Authors: Radhakrishnan, I. / Patel, D.J.
History
DepositionMay 24, 1994Processing site: BNL
Revision 1.0Oct 15, 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
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: DNA (5'-D(*GP*AP*AP*CP*AP*GP*GP*TP*TP*TP*TP*T*CP*CP*TP*GP*TP*TP*CP*TP*TP*TP*TP*T*CP*TP*TP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)9,4071
Polymers9,4071
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)6 / 6all calculated structures submitted
Representative

-
Components

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


Mass: 9407.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: MOLECULAR DYNAMICS, DISTANCE GEOMETRY / Software ordinal: 1
Details: NUMBER OF NUCLEIC ACID ATOMS -- 415 RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE CONDUCTED ON IDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION IN THE SEQUENCE WAS ...Details: NUMBER OF NUCLEIC ACID ATOMS -- 415 RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE CONDUCTED ON IDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION IN THE SEQUENCE WAS CONSIDERED. SIX STRUCTURES WERE CALCULATED INITIALLY USING DISTANCE RESTRAINTS. A MAJORITY OF THE DISTANCE RESTRAINTS WERE SUBSEQUENTLY REPLACED BY NOE INTENSITY RESTRAINTS. THE R(1/6) VALUE WAS MONITORED DURING THE REFINEMENTS. EACH STRUCTURE WAS SUBJECTED TO 500 CYCLES OF ENERGY MINIMIZATION AFTER THE DYNAMICS. NO AVERAGE STRUCTURE WAS CALCULATED. THE R(1/6) VALUE FOR THE MINIMIZED STRUCTURE REPRESENTING THE ENSEMBLE IS 0.024. THE DYNAMICS SIMULATIONS WERE PERFORMED IN THE PRESENCE OF EXPLICIT SOLVENT MOLECULES AND 15 NA+ COUNTER IONS. THE SUMMATION EXTENDS THROUGH ALL ASSIGNABLE, QUANTIFIABLE CROSS PEAK INTENSITIES IN NOESY SPECTRA RECORDED AT MIXING TIMES OF 40, 90 AND 150 MS. RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR THE MINIMIZED STRUCTURE `RM' REPRESENTING THE ENSEMBLE ARE AS FOLLOWS: RM BOND (ANGSTROMS) 0.016 (0.016) ANGLES (DEGREES) 3.825 (3.734) IMPROPERS (DEGREES) 0.552 (0.391) THE VALUES IN PARENTHESES CORRESPOND TO THE AVERAGE VALUES FOR THE ENSEMBLE OF SIX STRUCTURES.
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 6 / Conformers submitted total number: 6

+
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