1O59 | pdb_00001o59

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.222 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

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This is version 1.5 of the entry. See complete history. 


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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allantoicase355Saccharomyces cerevisiaeMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25335
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.209α = 90
b = 107.209β = 90
c = 134.918γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
CCP4data scaling
RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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