4JI5 Crystal Structure of 30S ribosomal subunit from Thermus thermophilus date
authors Demirci, H., Wang, L., IV, F.Murphy., Murphy, E., Carr, J., Blanchard, S., Jogl, G., Dahlberg, A.E., Gregory, S.T.
compound source
symmetry
R_factor
R_Free 0.2020
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.85
ligand 0TD, 2MG, 4OC, 5MC, 7MG, M2G, MA6, MG, PSU, UR3, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


Primary referenceThe central role of protein S12 in organizing the structure of the decoding site of the ribosome., Demirci H, Wang L, Murphy FV 4th, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST, RNA. 2013 Oct 23. PMID:24152548
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2291 Kb) [Save to disk]
  • Biological Unit Coordinates (4ji5.pdb1.gz) 2249 Kb
  • LPC: Ligand-Protein Contacts for 4JI5
  • CSU: Contacts of Structural Units for 4JI5
  • Structure Factors (1357 Kb)
  • Retrieve 4JI5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JI5 from S2C, [Save to disk]
  • Re-refined 4ji5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4JI5 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 4JI5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4JI5, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ji5_J] [4ji5_A] [4ji5_G] [4ji5_E] [4ji5_U] [4ji5_M] [4ji5_I] [4ji5_D] [4ji5_K] [4ji5_F] [4ji5_C] [4ji5_Q] [4ji5_O] [4ji5_S] [4ji5_N] [4ji5_P] [4ji5_H] [4ji5_R] [4ji5_T] [4ji5_L] [4ji5] [4ji5_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4JI5: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 4JI5
  • Community annotation for 4JI5 at PDBWiki (http://pdbwiki.org)

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