2PAQ

Crystal structure of the 5'-deoxynucleotidase YfbR

Structural Biology Knowledgebase: 2PAQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 2PAQ

Classification: HYDROLASE

Total Structure Weight: 46521.46

Macromolecule Entities
Molecule Chains Length Organism Details
5'-deoxynucleotidase YfbR A, B 201 Escherichia coli EC#: 3.1.3.89 IUBMB
Mutation: M1M, M22M, M39M, M66M, M107M, M175M, M179M
Gene Name(s): yfbR b2291 JW2288
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.187
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 137.02 α = 90.00
b = 137.02 β = 90.00
c = 56.29 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-27
  • Released Date: 2007-04-10
  • Deposition author(s): Zimmerman, M.D., Chruszcz, M., Cymborowski, M., Kudritska, M., Minor, W., Midwest Center for Structural Genomics (MCSG)
  • Previous versions: 1WPH

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 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: Source and taxonomy | Details: Removed strain from scientific name