1DK1

DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX

Structural Biology Knowledgebase: 1DK1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.213

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1DK1

Classification: RIBOSOME

Total Structure Weight: 29267.71


Macromolecule Entities
Molecule Chains Length Organism Details
30S RIBOSOMAL PROTEIN S15 A 86 Thermus thermophilus Fragment: RESIDUES 2-87
Mutation: I111M, A179M, M157M, M158M
Gene Name(s): rpsO rps15
Macromolecule Entities
Molecule Chains Length Organism Details
RRNA FRAGMENT B 57 Thermus thermophilus

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.213
  • Space Group: P 64 2 2

Unit Cell:

Length (Å) Angle (°)
a = 128.80 α = 90.00
b = 128.80 β = 90.00
c = 65.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-12-06
  • Released Date: 2000-04-02
  • Deposition author(s): Nikulin, A., Serganov, A., Ennifar, E., Tischenko, S., Nevskaya, N.

Revision History

  • 2011-12-28
    Type: Advisory | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4