3EB0 | pdb_00003eb0

Crystal Structure of cgd4_240 from cryptosporidium Parvum in complex with indirubin E804

• PDB DOI: https://doi.org/10.2210/pdb3EB0/pdb

• Classification: TRANSFERASE
• Organism(s): Cryptosporidium parvum Iowa II
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-26 Released: 2008-09-16 
• Deposition Author(s): Wernimont, A.K., Fedorov, O., Lam, A., Ali, A., Zhao, Y., Lew, J., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Wilstrom, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of cgd4_240 from cryptosporidium Parvum in complex with indirubin E804

Wernimont, A.K., Fedorov, O., Lam, A., Ali, A., Zhao, Y., Lew, J., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Wilstrom, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Lin, Y.H.

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.76 kDa 
• Atom Count: 5,221 
• Modeled Residue Count: 623 
• Deposited Residue Count: 766 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B [auth C]	383	Cryptosporidium parvum Iowa II	Mutation(s): 0  Gene Names: cgd4_240

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DRK	C [auth A], F [auth C]	3-({[(3S)-3,4-dihydroxybutyl]oxy}amino)-1H,2'H-2,3'-biindol-2'-one C20 H19 N3 O4 CKLAPOFDFZKCPB-LBPRGKRZSA-N
GOL	D [auth A], E [auth A], G [auth C], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
PTR	A, B [auth C]	TYR	Phosphorylation	C9 H12 N O6 P

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.101	α = 90
b = 138.366	β = 90
c = 43.261	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Wernimont, A.K., Fedorov, O., Lam, A., Ali, A., Zhao, Y., Lew, J., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Wilstrom, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-13
  Changes: Structure summary