3GDM | pdb_00003gdm

Crystal structure of the K93R mutant of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3GDM/pdb

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


• Deposited: 2009-02-24 Released: 2010-02-09 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wood, B.M., Gerlt, J.A., Almo, S.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the K93R mutant of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae.

Fedorov, A.A., Fedorov, E.V., Wood, B.M., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.62 kDa 
• Atom Count: 4,350 
• Modeled Residue Count: 510 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	267	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: URA3, YEL021W EC: 4.1.1.23
UniProt
Find proteins for P03962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03962  Go to UniProtKB:  P03962

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.642	α = 90
b = 93.141	β = 109.19
c = 67.233	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wood, B.M., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description