1O59 | pdb_00001o59

Crystal structure of Allantoicase (yir029w) from Saccharomyces cerevisiae at 2.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1O59/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-08-22 Released: 2003-09-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.222 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution

Xu, Q., Schwarzenbacher, R., Page, R., Sims, E., Abdubek, P., Ambing, E., Biorac, T., Brinen, L.S., Cambell, J., Canaves, J.M., Chiu, H.J., Dai, X., Deacon, A.M., DiDonato, M., Elsliger, M.A., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S.K., Hampton, E., Jaroszewski, L., Karlak, C., Klock, H.E., Koesema, E., Kovarik, J.S., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., McMullan, D., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Quijano, K., Reyes, R., Rezezadeh, F., Robb, A., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., von Delft, F., Wang, X., West, B., Wolf, G., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2004) Proteins 56: 619-624

• PubMed: 15229895 
• DOI: https://doi.org/10.1002/prot.20164
• Primary Citation Related Structures: 
  1O59

---

Organizational Affiliation: 
• The Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.46 kDa 
• Atom Count: 2,785 
• Modeled Residue Count: 318 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Allantoicase	A	355	Saccharomyces cerevisiae	Mutation(s): 5  Gene Names: YIR029W EC: 3.5.3.4
UniProt
Find proteins for P25335 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25335  Go to UniProtKB:  P25335

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.222 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31O59

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.209	α = 90
b = 107.209	β = 90
c = 134.918	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2003-09-02
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-12-20
  Changes: Database references
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary