2Q8L | pdb_00002q8l

Crystal structure of orotidine 5'-phosphate decarboxylase from Plasmodium falciparum

• PDB DOI: https://doi.org/10.2210/pdb2Q8L/pdb

• Classification: LYASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-11 Released: 2007-06-19 
• Deposition Author(s): Liu, Y., Lau, W., Lew, J., Amani, M., Hui, R., Pai, E.F., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of orotidine 5'-phosphate decarboxylase from Plasmodium falciparum.

Liu, Y., Lau, W., Lew, J., Amani, M., Hui, R., Pai, E.F.

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.

Macromolecule Content 

• Total Structure Weight: 37.96 kDa 
• Atom Count: 2,749 
• Modeled Residue Count: 314 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine-monophosphate-decarboxylase	A	323	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF10_0225 EC: 4.1.1.23
UniProt
Find proteins for Q8IJH3 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJH3  Go to UniProtKB:  Q8IJH3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.563	α = 90
b = 70.909	β = 90
c = 70.201	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Liu, Y., Lau, W., Lew, J., Amani, M., Hui, R., Pai, E.F., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description