1RB7

Yeast cytosine deaminase crystal form p212121 with sodium acetate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Microseed matrix screening to improve crystals of yeast cytosine deaminase.

Ireton, G.C.Stoddard, B.L.

(2004) Acta Crystallogr D Biol Crystallogr 60: 601-605

  • DOI: https://doi.org/10.1107/S0907444903029664
  • Primary Citation of Related Structures:  
    1RB7

  • PubMed Abstract: 

    A crystallization strategy termed 'microseed matrix screening' is described where the optimal conditions for nucleation versus extended lattice growth are not compatible. This method is an extension of conventional seeding techniques in which microseeds from the nucleation step are systematically seeded into new conditions where all components of the drop are allowed to vary to screen for subsequent growth of well ordered specimens. The structure of a crystal form of yeast cytosine deaminase produced by streak-seeding using a single condition for both nucleation and growth is compared with the structure of a related crystal form produced by separating nucleation and growth conditions. The resulting structural comparison demonstrates that differential chelation patterns of cations by acidic surface residues of proteins within crystal lattice contacts is a critical parameter of crystal nucleation and growth.


  • Organizational Affiliation

    Fred Hutchinson Cancer Research Center and the Graduate Program in Molecular and Cell Biology, University of Washington, 1100 Fairview Avenue North A3-023, Seattle, WA 98109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosine deaminase
A, B
161Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: FCY1YPR062WYP9499.17
EC: 3.5.4.1
UniProt
Find proteins for Q12178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12178 
Go to UniProtKB:  Q12178
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12178
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.489α = 90
b = 72.125β = 90
c = 79.441γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description