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PDBsum entry 1rb7

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1rb7
Jmol
Contents
Protein chains
152 a.a. *
Metals
_ZN ×4
Waters ×228
* Residue conservation analysis
PDB id:
1rb7
Name: Hydrolase
Title: Yeast cytosine deaminase crystal form p212121 with sodium acetate.
Structure: Cytosine deaminase. Chain: a, b. Synonym: cytosine aminohydrolase. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: fcy1, ypr062w, yp9499.17. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.185     R-free:   0.211
Authors: G.C.Ireton,B.L.Stoddard
Key ref:
G.C.Ireton and B.L.Stoddard (2004). Microseed matrix screening to improve crystals of yeast cytosine deaminase. Acta Crystallogr D Biol Crystallogr, 60, 601-605. PubMed id: 14993707 DOI: 10.1107/S0907444903029664
Date:
02-Nov-03     Release date:   02-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q12178  (FCY1_YEAST) -  Cytosine deaminase
Seq:
Struc:
158 a.a.
152 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.4.1  - Cytosine deaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cytosine + H2O = uracil + NH3
Cytosine
+ H(2)O
= uracil
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     UMP salvage   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444903029664 Acta Crystallogr D Biol Crystallogr 60:601-605 (2004)
PubMed id: 14993707  
 
 
Microseed matrix screening to improve crystals of yeast cytosine deaminase.
G.C.Ireton, B.L.Stoddard.
 
  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.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Calcium-mediated lattice contacts in crystal form II and the corresponding region in initial crystal form I. (a) A bound calcium ion is coordinated by surface side chains from three separate enzyme subunits: Glu75A and Gln150B from a physiological dimer and Glu128B' (green) from a subunit of a neighboring asymmetric unit. (b) In the presence of sodium in the initial crystallization condition (form I) no bound cation is visible and the corresponding side chains are further apart.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 601-605) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20445232 A.G.Villaseñor, A.Wong, A.Shao, A.Garg, A.Kuglstatter, and S.F.Harris (2010).
Acoustic matrix microseeding: improving protein crystal growth with minimal chemical bias.
  Acta Crystallogr D Biol Crystallogr, 66, 568-576.  
20693692 G.Obmolova, T.J.Malia, A.Teplyakov, R.Sweet, and G.L.Gilliland (2010).
Promoting crystallization of antibody-antigen complexes via microseed matrix screening.
  Acta Crystallogr D Biol Crystallogr, 66, 927-933.  
19145241 J.M.Kallio, N.Hakulinen, J.P.Kallio, M.H.Niemi, S.Kärkkäinen, and J.Rouvinen (2009).
The contribution of polystyrene nanospheres towards the crystallization of proteins.
  PLoS ONE, 4, e4198.  
18210369 B.A.Manjasetty, A.P.Turnbull, S.Panjikar, K.Büssow, and M.R.Chance (2008).
Automated technologies and novel techniques to accelerate protein crystallography for structural genomics.
  Proteomics, 8, 612-625.  
  18097093 T.S.Walter, E.J.Mancini, J.Kadlec, S.C.Graham, R.Assenberg, J.Ren, S.Sainsbury, R.J.Owens, D.I.Stuart, J.M.Grimes, and K.Harlos (2008).
Semi-automated microseeding of nanolitre crystallization experiments.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 14-18.  
16627479 J.R.Thompson, Z.C.Ryan, J.L.Salisbury, and R.Kumar (2006).
The structure of the human centrin 2-xeroderma pigmentosum group C protein complex.
  J Biol Chem, 281, 18746-18752.
PDB code: 2ggm
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.