[English] 日本語
Yorodumi
- PDB-1pc0: NMR Structure of the Archaeal Homologue of RNase P Protein Rpp29 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pc0
TitleNMR Structure of the Archaeal Homologue of RNase P Protein Rpp29
ComponentsHypothetical protein AF1917Hypothesis
KeywordsRNA BINDING PROTEIN / sandwich / beta-sheet
Function / homology
Function and homology information


ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / cytoplasm
Similarity search - Function
Ribonuclease P protein subunit RNP1 / Ribonuclease P/MRP subunit Rpp29 / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Rof/RNase P-like
Similarity search - Domain/homology
Ribonuclease P protein component 1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsSidote, D.J. / Hoffman, D.W.
CitationJournal: Biochemistry / Year: 2003
Title: NMR Structure of an Archaeal Homologue of Ribonuclease P Protein Rpp29
Authors: Sidote, D.J. / Hoffman, D.W.
History
DepositionMay 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein AF1917


Theoretical massNumber of molelcules
Total (without water)6,9001
Polymers6,9001
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Hypothetical protein AF1917 / Hypothesis


Mass: 6900.119 Da / Num. of mol.: 1 / Fragment: residue 17-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF1917 / Plasmid: pMAL-c2t / Production host: Escherichia coli (E. coli) / References: UniProt: O28362

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
3233D 13C-separated NOESY
2323D 15N-separated NOESY
4442D NOESY
5552D NOESY
6662D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM Rpp29 U-15N;10mM postassium phosphate pH 5.8 100mM sodium Chloride 10mM sodium azide90% H2O/10% D2O
21.8 mM Rpp29 U-15N;10mM postassium phosphate pH 3.0 100mM sodium Chloride 10mM sodium azide90% H2O/10% D2O
31.8 mM Rpp29 U-15N; U-13C; 10mM postassium phosphate pH 5.8 100mM sodium Chloride 10mM sodium azide90% H2O/10% D2O
41.8 mM Rpp29; 10mM postassium phosphate pH 5.8 100mM sodium Chloride 10mM sodium azide90% H2O/10% D2O
51.8 mM Rpp29; 10mM postassium phosphate pH 3.0 100mM sodium Chloride 10mM sodium azide90% H2O/10% D2O
61.8 mM Rpp29; 10mM postassium phosphate pH 5.8 100mM sodium Chloride 10mM sodium azide100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM 5.8 ambient 303 K
2100mM 3.0 ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger, A. T. / Classification: refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 651 restraints, 554 are NOE-derived distance constraints, 70 dihedral angle restraints,27 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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