2HW8

Structure of ribosomal protein L1-mRNA complex at 2.1 resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes.

Tishchenko, S.Nikonova, E.Nikulin, A.Nevskaya, N.Volchkov, S.Piendl, W.Garber, M.Nikonov, S.

(2006) ACTA CRYSTALLOGR.,SECT.D 62: 1545-1554

  • DOI: 10.1107/S0907444906041655

  • PubMed Abstract: 
  • The crystal structure of a hybrid complex between the bacterial ribosomal protein L1 from Thermus thermophilus and a Methanococcus vannielii mRNA fragment containing an L1-binding site was determined at 2.1 A resolution. It was found that all polar a ...

    The crystal structure of a hybrid complex between the bacterial ribosomal protein L1 from Thermus thermophilus and a Methanococcus vannielii mRNA fragment containing an L1-binding site was determined at 2.1 A resolution. It was found that all polar atoms involved in conserved protein-RNA hydrogen bonds have high values of density in the electron-density map and that their hydrogen-bonding capacity is fully realised through interactions with protein atoms, water molecules and K(+) ions. Intermolecular contacts were thoroughly analyzed in the present crystals and in crystals of previously determined L1-RNA complexes. It was shown that extension of the RNA helices providing canonical helix stacking between open-open or open-closed ends of RNA fragments is a common feature of these and all known crystals of complexes between ribosomal proteins and RNAs. In addition, the overwhelming majority of complexes between ribosomal proteins and RNA molecules display crystal contacts formed by the central parts of the RNA fragments. These contacts are often very extensive and strong and it is proposed that they are formed in the saturated solution prior to crystal formation.


    Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
A
228Thermus thermophilusMutation(s): 0 
Gene Names: rplA (rpl1)
Find proteins for P27150 (Thermus thermophilus)
Go to UniProtKB:  P27150
Entity ID: 1
MoleculeChainsLengthOrganism
36-MERB36N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
BU1
Query on BU1

Download SDF File 
Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.212 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.870α = 90.00
b = 67.870β = 90.00
c = 340.470γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
XDSdata reduction
CNSrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance