[English] 日本語
Yorodumi
- PDB-1xsg: Solution structure of E.coli RNase P RNA P4 stem oligoribonucleot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xsg
TitleSolution structure of E.coli RNase P RNA P4 stem oligoribonucleotide, U69A mutation
ComponentsRNase P RNA P4 stem
KeywordsRNA / Ribonuclease P RNA / Ribozyme / transfer RNA processing / P4 stem / U69A mutant / metal binding site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics, simulated annealing
Model type detailsminimized average
AuthorsSchmitz, M.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy
Authors: Schmitz, M.
History
DepositionOct 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNase P RNA P4 stem


Theoretical massNumber of molelcules
Total (without water)8,6561
Polymers8,6561
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 / -
RepresentativeModel #1minimized average structure

-
Components

#1: RNA chain RNase P RNA P4 stem


Mass: 8656.183 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: enzymatically synthesized from DNA oligonucleotide template by T7 RNA polymerase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
132DQF-COSY
14231P-1H-HETERO-COSY
15231P-1H-HETERO-TOCSY-NOESY
NMR detailsText: The structure was determined using standard 2D homonuclear techniques as well as 13C and 31P heteronuclear experiments performed at natural abundance

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer pH 6.4; 90% H2O, 10% D2O90% H2O/10% D2O
22mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer pH 6.4; 100% D2O100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.4 / Pressure: ambient / Temperature: 288 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.2Brukercollection
NMRPipe2.1F. Delaglioprocessing
X-PLOR3.1structure solution
X-PLOR3.1refinement
RefinementMethod: restrained molecular dynamics, simulated annealing / Software ordinal: 1
Details: The average structure is based on the superposition of 12 structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.78 Angstrom. A total of ...Details: The average structure is based on the superposition of 12 structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.78 Angstrom. A total of 290 NOE-derived distance constraints, 245 dihedral restraints and 48 distance restraints from hydrogen bonds were used in refinement.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers 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