1DD3 Ribosome date Nov 08, 1999
title Crystal Structure Of Ribosomal Protein L12 From Thermotoga M
authors M.C.Wahl, G.P.Bourenkov, H.D.Bartunik, R.Huber
compound source
Molecule: 50s Ribosomal Protein L7l12
Chain: A, B
 Organism_scientific: Thermotoga Maritima
Organism_taxid: 2336

Molecule: 50s Ribosomal Protein L7l12
Chain: C, D
Organism_scientific: Thermotoga Maritima
Organism_taxid: 2336
symmetry Space Group: C 2 2 21
R_factor 0.226 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.330 89.130 119.630 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
related structures by homologous chain: 1DD4
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceFlexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12., Wahl MC, Bourenkov GP, Bartunik HD, Huber R, EMBO J 2000 Jan 17;19(2):174-86. PMID:10637222
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (1dd3.pdb1.gz) 52 Kb
  • CSU: Contacts of Structural Units for 1DD3
  • Likely Quarternary Molecular Structure file(s) for 1DD3
  • Retrieve 1DD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DD3 from S2C, [Save to disk]
    • View 1DD3 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1DD3
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1DD3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dd3a1, region A:1-57 [Jmol] [rasmolscript] [script source]
        - Domain d1dd3a2, region A:58-128 [Jmol] [rasmolscript] [script source]
        - Domain d1dd3b1, region B:1-57 [Jmol] [rasmolscript] [script source]
        - Domain d1dd3b2, region B:58-128 [Jmol] [rasmolscript] [script source]
        - Domain d1dd3c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1dd3d_, region D [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dd3] [1dd3_B] [1dd3_D] [1dd3_A] [1dd3_C]
  • SWISS-PROT database: [P29396]
  • Domain organization of [RL7_THEMA] by SWISSPFAM
    • Other resources with information on 1DD3
  • Community annotation for 1DD3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Domain movements in 1DD3 from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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