1TQX | pdb_00001tqx

Crystal Structure of Pfal009167 A Putative D-Ribulose 5-Phosphate 3-Epimerase from P.falciparum

• PDB DOI: https://doi.org/10.2210/pdb1TQX/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-06-18 Released: 2004-12-21 
• Deposition Author(s): Caruthers, J., Bosch, J., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum.

Caruthers, J., Bosch, J., Buckner, F., Van Voorhis, W., Myler, P., Worthey, E., Mehlin, C., Boni, E., DeTitta, G., Luft, J., Lauricella, A., Kalyuzhniy, O., Anderson, L., Zucker, F., Soltis, M., Hol, W.G.

(2006) Proteins 62: 338-342

• PubMed: 16304640 
• DOI: https://doi.org/10.1002/prot.20764
• Primary Citation Related Structures: 
  1TQX


• PubMed Abstract: 
  

  The crystal structure of Pfal009167AAA, a putative ribulose 5-phosphate 3-epimerase (PfalRPE) from Plasmodium falciparum, has been determined to 2 A resolution. RPE represents an exciting potential drug target for developing antimalarials because it is involved in the shikimate and the pentose phosphate pathways. The structure is a classic TIM-barrel fold. A coordinated Zn ion and a bound sulfate ion in the active site of the enzyme allow for a greater understanding of the mechanism of action of this enzyme. This structure is solved in the framework of the Structural Genomics of Pathogenic Protozoa (SGPP) consortium.

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Organizational Affiliation: 
• SLAC, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.48 kDa 
• Atom Count: 3,752 
• Modeled Residue Count: 442 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ribulose-5-phosphate 3-epimerase, putative	A, B	227	Plasmodium falciparum 3D7	Mutation(s): 0  EC: 5.1.3.1
UniProt
Find proteins for Q8I5L3 (Plasmodium falciparum (isolate 3D7)) Explore Q8I5L3  Go to UniProtKB:  Q8I5L3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.415	α = 90
b = 84.454	β = 90
c = 120.717	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Caruthers, J., Bosch, J., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description