2QGA | pdb_00002qga

Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound

• PDB DOI: https://doi.org/10.2210/pdb2QGA/pdb

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


• Deposited: 2007-06-28 Released: 2007-07-24 
• Deposition Author(s): Lunin, V.V., Wernimont, A.K., Lew, J., Kozieradzki, I., Bochkarev, A., Arrowsmith, C.H., Sundstrom, M., Weigelt, J., Edwards, A.E., Hui, R., Hills, T., Altamentova, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.210 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound

Lunin, V.V., Wernimont, A.K., Lew, J., Kozieradzki, I., Bochkarev, A., Arrowsmith, C.H., Sundstrom, M., Weigelt, J., Edwards, A.E., Hui, R., Hills, T., Altamentova, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 107.65 kDa 
• Atom Count: 8,242 
• Modeled Residue Count: 909 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate lyase	A [auth B], B [auth C]	465	Plasmodium vivax	Mutation(s): 0  Gene Names: asl EC: 4.3.2.2
UniProt
Find proteins for A5KBL5 (Plasmodium vivax (strain Salvador I)) Explore A5KBL5  Go to UniProtKB:  A5KBL5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	F [auth B], J [auth C]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	D [auth B], E [auth B], H [auth C], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	C [auth B], G [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.210 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.247	α = 90
b = 179.545	β = 99.37
c = 68.575	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Lunin, V.V., Wernimont, A.K., Lew, J., Kozieradzki, I., Bochkarev, A., Arrowsmith, C.H., Sundstrom, M., Weigelt, J., Edwards, A.E., Hui, R., Hills, T., Altamentova, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description