3QYQ

1.8 Angstrom resolution crystal structure of a putative deoxyribose-phosphate aldolase from Toxoplasma gondii ME49

• PDB DOI: https://doi.org/10.2210/pdb3QYQ/pdb

• Classification: LYASE
• Organism(s): Toxoplasma gondii ME49
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-03 Released: 2011-03-30 
• Deposition Author(s): Halavaty, A.S., Ruan, J., Minasov, G., Shuvalova, L., Ueno, A., Igarashi, M., Ngo, H., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

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: 130.21 kDa 
• Atom Count: 9,940 
• Modelled Residue Count: 1,084 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribose-phosphate aldolase, putative	A, B, C, D	293	Toxoplasma gondii ME49	Mutation(s): 0  Gene Names: TGME49_118750 EC: 4.1.2.4
UniProt
Find proteins for B9PVB4 (Toxoplasma gondii (strain ATCC 50861 / VEG)) Explore B9PVB4  Go to UniProtKB:  B9PVB4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	E, F, G	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth D], V [auth D], W [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	E, F, G	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M33QYQ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.923	α = 62.9
b = 72.194	β = 89.8
c = 73.048	γ = 88.85

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-30 
Deposition Author(s): Halavaty, A.S., Ruan, J., Minasov, G., Shuvalova, L., Ueno, A., Igarashi, M., Ngo, H., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-15
  Changes: Refinement description
• Version 1.3: 2014-11-12
  Changes: Database references
• Version 1.4: 2015-04-08
  Changes: Database references
• Version 1.5: 2017-11-08
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary