2Z70

E.coli RNase 1 in complex with d(CGCGATCGCG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli

Rodriguez, S.M.Panjikar, S.Van Belle, K.Wyns, L.Messens, J.Loris, R.

(2008) Protein Sci. 17: 681-690

  • DOI: 10.1110/ps.073420708

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli ribonuclease I (EcRNase I) reveals an RNase T2-type fold consisting of a conserved core of six beta-strands and three alpha-helices. The overall architecture of the catalytic residues is very similar to the p ...

    The crystal structure of Escherichia coli ribonuclease I (EcRNase I) reveals an RNase T2-type fold consisting of a conserved core of six beta-strands and three alpha-helices. The overall architecture of the catalytic residues is very similar to the plant and fungal RNase T2 family members, but the perimeter surrounding the active site is characterized by structural elements specific for E. coli. In the structure of EcRNase I in complex with a substrate-mimicking decadeoxynucleotide d(CGCGATCGCG), we observe a cytosine bound in the B2 base binding site and mixed binding of thymine and guanine in the B1 base binding site. The active site residues His55, His133, and Glu129 interact with the phosphodiester linkage only through a set of water molecules. Residues forming the B2 base recognition site are well conserved among bacterial homologs and may generate limited base specificity. On the other hand, the B1 binding cleft acquires true base aspecificity by combining hydrophobic van der Waals contacts at its sides with a water-mediated hydrogen-bonding network at the bottom. This B1 base recognition site is highly variable among bacterial sequences and the observed interactions are unique to EcRNaseI and a few close relatives.


    Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vrije Universiteit Brussels, Pleinlaan 2, B-1050 Brussels, Belgium.




Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease I
A
245Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rna (rnsA)
EC: 4.6.1.21
Find proteins for P21338 (Escherichia coli (strain K12))
Go to UniProtKB:  P21338
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DTP*DCP*DGP*DCP*DG)-3')B7N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.556α = 90.00
b = 49.758β = 90.00
c = 143.108γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2008-07-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Version format compliance