[English] 日本語
Yorodumi
- PDB-2k3f: Ribosomal protein L11 from Thermotoga maritima -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k3f
TitleRibosomal protein L11 from Thermotoga maritima
Components50S ribosomal protein L11
KeywordsRIBOSOMAL PROTEIN / L11 / Methylation / Ribonucleoprotein / RNA-binding
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal ...Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsNMR solution structure of the free form L11 ribosomal protein from Thermotoga maritima - refined ...NMR solution structure of the free form L11 ribosomal protein from Thermotoga maritima - refined and recalculated using CNS with allhdg5.3 forecefield
AuthorsJonker, H.R.A. / Ilin, S. / Schwalbe, H. / Woehnert, J.
Citation
Journal: ChemBioChem / Year: 2005
Title: Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima
Authors: Ilin, S. / Hoskins, A. / Ohlenschlager, O. / Jonker, H.R.A. / Schwalbe, H. / Woehnert, J.
#1: Journal: Nucleic Acids Res. / Year: 2007
Title: L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy
Authors: Jonker, H.R.A. / Ilin, S. / Grimm, S.K. / Woehnert, J. / Schwalbe, H.
History
DepositionMay 6, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
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: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)15,1121
Polymers15,1121
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)20 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein 50S ribosomal protein L11


Mass: 15111.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rplK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29395

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution structure of the free form L11 ribosomal protein from Thermotoga maritima - refined and recalculated using CNS with allhdg5.3 forecefield
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
131IPAP(1H,15N)HSQC
141IPAP(1H,15N)HSQC

-
Sample preparation

DetailsContents: 1.2 mM [U-100% 15N] L11, 20 mM potassium phosphate, 50 mM potassium chloride, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mML11[U-100% 15N]1
20 mMpotassium phosphate1
50 mMpotassium chloride1
10 %D2O[U-100% 2H]1
Sample conditionsIonic strength: 70 / pH: 6.1 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA7504

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Bruker Biospincollection
XwinNMR3Bruker Biospinprocessing
VNMRVariancollection
VNMRVarianprocessing
XEASYBartels et al.data analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA1.2Nilgesrefinement
ARIA1.2Nilgesstructure solution
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: Initial coordinates are calculated by CNS and further refinement in water has been performed using ARIA protocols with additional diffusion anisotropy data
NMR constraintsNOE constraints total: 3663 / NOE intraresidue total count: 981
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / 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://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