[English] 日本語
Yorodumi
- PDB-1njp: The crystal structure of the 50S Large ribosomal subunit from Dei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1njp
TitleThe crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM)
Components
  • 23S ribosomal RNA
  • 50S ribosomal protein L16
  • GENERAL STRESS PROTEIN CTC
  • tRNA acceptor stem mimic
KeywordsRIBOSOME / Ribosomes / tRNA / puromycin / sparsomycin / peptidyl-transferase / peptide bond formation
Function / homology
Function and homology information


5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal L25p family / Ribosomal protein L25 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L16 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBashan, A. / Agmon, I. / Zarivatch, R. / Schluenzen, F. / Harms, J.M. / Berisio, R. / Bartels, H. / Hansen, H.A. / Yonath, A.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural basis of the ribosomal machinery for Peptide bond formation, translocation, and nascent chain progression
Authors: Bashan, A. / Agmon, I. / Zarivatch, R. / Schluenzen, F. / Harms, J.M. / Berisio, R. / Bartels, H. / Franceschi, F. / Auerbach, T. / Hansen, H.A. / Kossoy, E. / Kessler, M. / Yonath, A.
History
DepositionJan 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: 23S ribosomal RNA
5: tRNA acceptor stem mimic
K: 50S ribosomal protein L16
T: GENERAL STRESS PROTEIN CTC


Theoretical massNumber of molelcules
Total (without water)986,3384
Polymers986,3384
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.9, 409.9, 695.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

-
Components

#1: RNA chain 23S ribosomal RNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 6460405
#2: RNA chain tRNA acceptor stem mimic


Mass: 11391.945 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The terminal C of ASM was coupled via a phosphodiester bond to the 5 OH of the N6-dimethyl moiety of puromycin
#3: Protein 50S ribosomal protein L16 / Coordinate model: Cα atoms only


Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ5
#4: Protein GENERAL STRESS PROTEIN CTC / Coordinate model: Cα atoms only


Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RX88

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 64 %
Crystal growpH: 7.8
Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM , pH 7.80
Components of the solutions
IDNameCrystal-IDSol-ID
1ETHANOL11
2DIMETHYLHEXANEDIOL11
3MGCL211
4KCL11
5NH4CL11
6SPARSOMYCIN11
7HEPES11
8ETHANOL12
9DIMETHYLHEXANEDIOL12
10MGCL212
11KCL12
12NH4CL12
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion
Details: Harms, J.M., (2001) Cell (Cambridge,Mass.), 107, 679.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1reservoirMgCl2
260 mM1reservoirNH4Cl
35 mM1reservoirKCl
410 mMHEPES1reservoirpH7.8
51
61
71
81
91
101
111
121

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 290998 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Rsym value: 0.125 / Net I/σ(I): 4.6
Reflection shellResolution: 3.5→3.63 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.384 / % possible all: 98.6
Reflection
*PLUS
Rmerge(I) obs: 0.125
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.384

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NKW

1nkw


Resolution: 3.5→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.295 13300 5 %random
Rwork0.244 ---
obs0.2441 266007 --
all-266007 --
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms347 59902 0 0 60249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d0.97
X-RAY DIFFRACTIONc_angle_deg0.97
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Rfactor Rfree: 0.303
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_d

+
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