[English] 日本語
Yorodumi
- PDB-2o44: Structure of 23S rRNA of the large ribosomal subunit from Deinoco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o44
TitleStructure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide josamycin
Components23S rRNA23S ribosomal RNA
KeywordsRNA / ribosome / macrolides
Function / homologyChem-JOS / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPyetan, E. / Daram, D. / Auerbach-Nevo, T. / Yonath, A.
CitationJournal: TO BE PUBLISHED
Title: Chemical parameters influencing fine tuning in the binding of Macrolide antibiotics to the ribosomal tunnel
Authors: Pyetan, E. / Baram, D. / Auerbach-Nevo, T. / Yonath, A.
History
DepositionDec 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Advisory
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)934,2332
Polymers933,4051
Non-polymers8281
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.802, 411.475, 697.616
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Detailsthe large ribosomal subunit from Deinococcus radiodurans and the macrolide josamycin

-
Components

#1: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
#2: Chemical ChemComp-JOS / (2S,3S,4R,6S)-6-{[(2R,3S,4R,5R,6S)-6-{[(4R,5S,6S,7R,9R,10S,12E,14Z,16R)-4-(ACETYLOXY)-10-HYDROXY-5-METHOXY-9,16-DIMETHYL-2-OXO-7-(2-OXOETHYL)OXACYCLOHEXADECA-12,14-DIEN-6-YL]OXY}-4-(DIMETHYLAMINO)-5-HYDROXY-2-METHYLTETRAHYDRO-2H-PYRAN-3-YL]OXY}-4-HYDROXY-2,4-DIMETHYLTETRAHYDRO-2H-PYRAN-3-YL 3-METHYLBUTANOATE / JOSAMYCIN / Josamycin


Mass: 827.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H69NO15 / Comment: antibiotic*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 6.64 Å3/Da / Density % sol: 81.48 %

-
Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 19-ID1
SYNCHROTRONESRF ID292
Detector
IDDetector
1CCD
2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 345218 / Observed criterion σ(I): 1.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.184

-
Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NKW

1nkw


Resolution: 3.3→8 Å / σ(F): 1.5 / σ(I): 1.5 /
RfactorNum. reflection
Rfree0.3305 -
all0.282 -
obs-345218
Refinement stepCycle: LAST / Resolution: 3.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 59359 58 0 59417

+
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