1YOE

Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose

Muzzolini, L.Versees, W.Steyaert, J.Degano, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein ybeK
A
322Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rihA (ybeK)
EC: 3.2.-.-
Find proteins for P41409 (Escherichia coli (strain K12))
Go to UniProtKB:  P41409
Small Molecules
Ligands 2 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
RIB
Query on RIB

Download SDF File 
Download CCD File 
A
RIBOSE
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.466α = 90.00
b = 84.062β = 90.00
c = 112.483γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance