[English] 日本語
Yorodumi
- PDB-2kco: Solution NMR structure of ribosomal protein sso0164 from Sulfolob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kco
TitleSolution NMR structure of ribosomal protein sso0164 from Sulfolobus solfataricus. Northeast Structural Genomics Consortium (NESG) target SsT4.
Components30S ribosomal protein S8e
KeywordsRIBOSOMAL PROTEIN / ribosomal protein of unknown function / Ribonucleoprotein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic small ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Thrombin, subunit H - #310 / Ribosomal protein S8e, archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S8e / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
30S ribosomal protein S8e
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodSOLUTION NMR / restrained molecular dynamics in water bath
Model detailslowest energy, model 1
AuthorsLemak, A. / Gutmanas, A. / Yee, A. / Fares, C. / Garcia, M. / Montelione, G.T. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of ribosomal protein sso0164 from Sulfolobus solfataricus
Authors: Lemak, A. / Gutmanas, A. / Yee, A. / Fares, C. / Garcia, M. / Montelione, G.T. / Arrowsmith, C.H.
History
DepositionDec 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 30S ribosomal protein S8e


Theoretical massNumber of molelcules
Total (without water)14,6861
Polymers14,6861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein 30S ribosomal protein S8e


Mass: 14685.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: DSM 1617 / JCM 11322 / P2 / Gene: rps8e, SSO0164 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q980W3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D H(CCO)NH
1613D C(CO)NH
1713D 1H-15N NOESY
1813D (H)CCH-TOCSY
1913D (H)CCH-TOCSY
11013D 1H-13C NOESY
11113D 1H-13C arom NOESY
11212D 1H-15N HSQC(IPAP)
NMR detailsText: The NMR data suggest that residues 1-60 do not form a globular domain, although residues 38-48 does form an isolated helix. This N-terminal region is likely to be very flexible and the extended ...Text: The NMR data suggest that residues 1-60 do not form a globular domain, although residues 38-48 does form an isolated helix. This N-terminal region is likely to be very flexible and the extended structures presented here do not necessarily represent a defined conformation for this region (other than the helix). There do not appear to be any interactions between residues 1-60 and the C-terminal globular part of the protein.

-
Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] sso0164-1, 10 mM TRIS-2, 500 mM sodium chloride-3, 10 uM ZnSO4-4, 10 mM DTT-5, 0.01 % NaN3-6, 10 mM benzamidine-7, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMsso0164-1[U-13C; U-15N]1
10 mMTRIS-21
500 mMsodium chloride-31
10 uMZnSO4-41
10 mMDTT-51
0.01 %NaN3-61
10 mMbenzamidine-71
Sample conditionsIonic strength: 500 / pH: 7.7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE6003

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak, Steren, Llinas, Arrowsmithresonanmce assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: restrained molecular dynamics in water bath / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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