[English] 日本語
Yorodumi
- PDB-1l3m: The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l3m
TitleThe Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2
Components5'-D(*CP*GP*C)-R(P*(A39)P*(A39)P*(A39))-D(P*TP*TP*TP*GP*CP*G)-3'
KeywordsDNA/RNA / DNA/RNA HYBRID / CHIMERIC DUPLEX / 2'O-methyl / DNA-RNA complex
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodSOLUTION NMR / SA, MD, MATRIX RELAXATION REFINEMENT
AuthorsTsao, Y.P. / Wang, L.Y. / Hsu, S.T. / Jain, M.L. / Chou, S.H. / Huang, W.C. / Cheng, J.W.
CitationJournal: J.Biomol.NMR / Year: 2001
Title: The solution structure of [d(CGC)r(amamam)d(TTTGCG)]2.
Authors: Tsao, Y.P. / Wang, L.Y. / Hsu, S.T. / Jain, M.L. / Chou, S.H. / Huang, C. / Cheng, J.W.
History
DepositionFeb 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*GP*C)-R(P*(A39)P*(A39)P*(A39))-D(P*TP*TP*TP*GP*CP*G)-3'
B: 5'-D(*CP*GP*C)-R(P*(A39)P*(A39)P*(A39))-D(P*TP*TP*TP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,5052
Polymers7,5052
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 / 10THE SUBMITTED CONFORMER MODELS ARE THE 10 STRUCTURES WITH THE LOWEST ENERGY.
RepresentativeModel #4the structure with the lowest energy was selected

-
Components

#1: DNA/RNA hybrid 5'-D(*CP*GP*C)-R(P*(A39)P*(A39)P*(A39))-D(P*TP*TP*TP*GP*CP*G)-3'


Mass: 3752.482 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED FROM 2D NMR SPECTROSCOPY WITH UNLABELED SAMPLE.

-
Sample preparation

DetailsContents: 20 mM sodium phosphate, 200 mM NaCl and 0.05 mM EDTA (pH 7.0) 100% D2O OR 90% H2O:10% D2O
Solvent system: 100% D2O OR 90% H2O:10% D2O
Sample conditionspH: 7 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERstructure solution
X-PLOR3.851BRUNGERrefinement
RefinementMethod: SA, MD, MATRIX RELAXATION REFINEMENT / Software ordinal: 1
Details: Three-dimensional structures were calculated using 454 NOE distance restraints, 30 hydrogen bond restraints, and 208 backbone, sugar, and glycosidic dihedral angle restraints.
NMR representativeSelection criteria: the structure with the lowest energy was selected
NMR ensembleConformer selection criteria: THE SUBMITTED CONFORMER MODELS ARE THE 10 STRUCTURES WITH THE LOWEST ENERGY.
Conformers calculated total number: 10 / 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