2F8M | pdb_00002f8m

Ribose 5-phosphate isomerase from Plasmodium falciparum

• PDB DOI: https://doi.org/10.2210/pdb2F8M/pdb

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


• Deposited: 2005-12-02 Released: 2005-12-27 
• Deposition Author(s): Holmes, M.A., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.272 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.218 (DCC) 

Starting Model: experimental

Literature

Structure of ribose 5-phosphate isomerase from Plasmodium falciparum.

Holmes, M.A., Buckner, F.S., Van Voorhis, W.C., Verlinde, C.L., Mehlin, C., Boni, E., DeTitta, G., Luft, J., Lauricella, A., Anderson, L., Kalyuzhniy, O., Zucker, F., Schoenfeld, L.W., Earnest, T.N., Hol, W.G., Merritt, E.A.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 427-431

• PubMed: 16682767 
• DOI: https://doi.org/10.1107/S1744309106010876
• Primary Citation Related Structures: 
  2F8M


• PubMed Abstract: 
  

  The structure of ribose 5-phosphate isomerase from Plasmodium falciparum, PFE0730c, has been determined by molecular replacement at 2.09 angstroms resolution. The enzyme, which catalyzes the isomerization reaction that interconverts ribose 5-phosphate and ribulose 5-phosphate, is a member of the pentose phosphate pathway. The P. falciparum enzyme belongs to the ribose 5-phosphate isomerase A family, Pfam family PF06562 (DUF1124), and is structurally similar to other members of the family.

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Organizational Affiliation: 
• Structural Genomics of Pathogenic Protozoa (SGPP) Consortium, USA.

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: 54.66 kDa 
• Atom Count: 3,831 
• Modeled Residue Count: 472 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ribose 5-phosphate isomerase	A, B	244	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PFE0730c EC: 5.3.1.6
UniProt
Find proteins for Q8I3W2 (Plasmodium falciparum (isolate 3D7)) Explore Q8I3W2  Go to UniProtKB:  Q8I3W2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.272 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.218 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.689	α = 90
b = 136.23	β = 90
c = 45.011	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-27 
Deposition Author(s): Holmes, M.A., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2005-12-27
  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: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description