3D8K | pdb_00003d8k

Crystal structure of a phosphatase from a toxoplasma gondii

• PDB DOI: https://doi.org/10.2210/pdb3D8K/pdb

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


• Deposited: 2008-05-23 Released: 2008-06-17 
• Deposition Author(s): Damodharan, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.304 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

Crsytal structure of a phosphatase from a toxoplasma gondii

Damodharan, L., Sauder, J.M., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 168.44 kDa 
• Atom Count: 10,892 
• Modeled Residue Count: 1,395 
• Deposited Residue Count: 1,508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phosphatase 2C	A, B, C, D	377	Toxoplasma gondii	Mutation(s): 0  Gene Names: pp2c EC: 3.1.3.16
UniProt
Find proteins for A4GX63 (Toxoplasma gondii) Explore A4GX63  Go to UniProtKB:  A4GX63

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.71 Å
• R-Value Free:  0.304 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.882	α = 90
b = 169.052	β = 104.47
c = 87.012	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SOLVE	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Damodharan, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-02
  Changes: Structure summary
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2018-11-14
  Changes: Data collection, Database references
• Version 1.5: 2019-01-16
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2024-11-20
  Changes: Data collection, Database references, Structure summary