2PXP

Variant 13 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A General Strategy to Solve the Phase Problem in RNA Crystallography.

Keel, A.Y.Rambo, R.P.Batey, R.T.Kieft, J.S.

(2007) Structure 15: 761-772

  • DOI: 10.1016/j.str.2007.06.003
  • Primary Citation of Related Structures:  2PXB, 2PXD, 2PXE, 2PXF, 2PXK, 2PXL, 2PXQ, 2PXT, 2PXU, 2PXV

  • PubMed Abstract: 
  • X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding heavy-atom derivatives to obtain high-quality experimental phase information. Existing techniques have drawbacks, limiting the ...

    X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding heavy-atom derivatives to obtain high-quality experimental phase information. Existing techniques have drawbacks, limiting the rate at which important new structures are solved. To address this, we have developed a reliable means to localize heavy atoms specifically to virtually any RNA. By solving the crystal structures of thirteen variants of the G*U wobble pair cation binding motif, we have identified a version that when inserted into an RNA helix introduces a high-occupancy cation binding site suitable for phasing. This "directed soaking" strategy can be integrated fully into existing RNA crystallography methods, potentially increasing the rate at which important structures are solved and facilitating routine solving of structures using Cu-Kalpha radiation. This method already has been used to solve several crystal structures.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle protein
A
102Escherichia coli (strain K12)Gene Names: ffh
Find proteins for P0AGD7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGD7
Entity ID: 1
MoleculeChainsLengthOrganism
4.5 S RNAB49N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
B
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 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: 2.5 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.345α = 90.00
b = 78.165β = 94.99
c = 32.566γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance