1YOE

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

Structural Biology Knowledgebase: 1YOE SBKB.org


Experimental Data Snapshot

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

Literature

Macromolecules
Sequence Display for 1YOE

Classification: Hydrolase

Total Structure Weight: 35318.63

Macromolecule Entities
Molecule Chains Length Organism Details
Hypothetical protein ybeK A 322 Escherichia coli Gene Name(s): rihA ybeK b0651 JW0646
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
RIB
Query on RIB

A RIBOSE
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 76.47 α = 90.00
b = 84.06 β = 90.00
c = 112.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-27
  • Released Date: 2006-01-17
  • Deposition author(s): Muzzolini, L., Versees, W., Steyaert, J., Degano, M.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values