[English] 日本語
Yorodumi
- PDB-1n53: SOLUTION STRUCTURE OF B. SUBTILIS T BOX ANTITERMINATOR RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n53
TitleSOLUTION STRUCTURE OF B. SUBTILIS T BOX ANTITERMINATOR RNA
Components
  • RNA (5'-R(*GP*AP*GP*GP*GP*UP*GP*GP*AP*AP*CP*CP*GP*CP*GP*C)-3')
  • RNA (5'-R(*GP*CP*GP*UP*CP*CP*CP*UP*C)-3')
KeywordsRNA / T box / bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsGerdeman, M.S. / Henkin, T.M. / Hines, J.V.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Solution Structure of the Bacillus subtilis T-box Antiterminator RNA: Seven Nucleotide Bulge Characterized by Stacking and Flexibility
Authors: Gerdeman, M.S. / Henkin, T.M. / Hines, J.V.
History
DepositionNov 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: RNA (5'-R(*GP*AP*GP*GP*GP*UP*GP*GP*AP*AP*CP*CP*GP*CP*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*UP*CP*CP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,0152
Polymers8,0152
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50The minimized average structure of the 9 lowest energy structures (all with favorable non-bond energy and the fewest number of constraint violations) is submitted.
RepresentativeModel #1

-
Components

#1: RNA chain RNA (5'-R(*GP*AP*GP*GP*GP*UP*GP*GP*AP*AP*CP*CP*GP*CP*GP*C)-3')


Mass: 5231.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized using T7 RNA polymerase
#2: RNA chain RNA (5'-R(*GP*CP*GP*UP*CP*CP*CP*UP*C)-3')


Mass: 2783.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized using T7 RNA polymerase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1413D 13C-separated NOESY
1512D HSQC
1612D 1H 31P HETCOR
NMR detailsText: This structure was determined using standard 2D and 3D homonuclear and heteronuclear NMR techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM (U-15N, U-13C) or 1.2 mM (unlabeled) T box model RNA (AM1A); 10 mM sodium phosphate buffer pH 6.5, 0.01 mM EDTA100% D2O
20.7 mM (U-15N, U-13C) or 1.2 mM (unlabeled) T box model RNA (AM1A); 10 mM sodium phosphate buffer pH 6.5, 0.01 mM EDTA90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM 6.5 ambient 295 K
210 mM 6.5 ambient 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX4002
Bruker DMXBrukerDMX6003

-
Processing

NMR software
NameVersionDeveloperClassification
Felix95,98processing
X-PLOR98.1Brungerstructure solution
XwinNMRprocessing
X-PLOR98.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: A total of 313 distance constraints and 59 dihedral angle constraints were used.
NMR ensembleConformer selection criteria: The minimized average structure of the 9 lowest energy structures (all with favorable non-bond energy and the fewest number of constraint violations) is submitted.
Conformers calculated total number: 50 / Conformers submitted total number: 1

+
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