2F84

Crystal Structure of an orotidine-5'-monophosphate decarboxylase homolog from P.falciparum

• PDB DOI: https://doi.org/10.2210/pdb2F84/pdb

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


• Deposited: 2005-12-01 Released: 2005-12-20 
• Deposition Author(s): Caruthers, J.M., Robein, M., Merritt, E.A., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.288 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Crystal Structure of an orotidine-5'-monophosphate decarboxylase homolog from Plasmodium falciparum

Caruthers, J.M., Robein, M., Zucker, F., Mehlin, C., Luft, J., Boni, E., Lauricella, A., Merritt, E.A., Hol, W.G.J.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 37.96 kDa 
• Atom Count: 2,787 
• Modelled Residue Count: 323 
• 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: NC_004314 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: 0.288 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.911	α = 90
b = 69.057	β = 90
c = 69.735	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-20 
Deposition Author(s): Caruthers, J.M., Robein, M., Merritt, E.A., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2005-12-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description