3E15 | pdb_00003e15

6-phosphogluconolactonase from Plasmodium vivax

• PDB DOI: https://doi.org/10.2210/pdb3E15/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-01 Released: 2008-08-19 
• Deposition Author(s): Arakaki, T.L., Merritt, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.202 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.150 (Depositor) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

6-phosphogluconolactonase from Plasmodium vivax

Arakaki, T.L., Merritt, E.A.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 147.07 kDa 
• Atom Count: 10,510 
• Modeled Residue Count: 1,176 
• Deposited Residue Count: 1,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate 1-dehydrogenase	A, B, C, D	312	Plasmodium vivax	Mutation(s): 0  Gene Names: PVX_117790 EC: 3.1.1.31 (PDB Primary Data), 1.1.1.49 (UniProt)
UniProt
Find proteins for A5K3M1 (Plasmodium vivax (strain Salvador I)) Explore A5K3M1  Go to UniProtKB:  A5K3M1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZI	G [auth A], I [auth B], K [auth C], N [auth D]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
K	F [auth A], H [auth B], J [auth C], M [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.202 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.150 (Depositor) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.524	α = 63.98
b = 80.846	β = 88.1
c = 89.765	γ = 80.01

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Arakaki, T.L., Merritt, E.A.

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-11-13
  Changes: Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary