3BE4

Crystal structure of Cryptosporidium parvum adenylate kinase cgd5_3360

• PDB DOI: https://doi.org/10.2210/pdb3BE4/pdb

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


• Deposited: 2007-11-16 Released: 2007-12-18 
• Deposition Author(s): Wernimont, A.K., Lew, J., Kozieradzki, I., Lin, Y.H., Sun, X., Khuu, C., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bochkarev, A., Hui, R., Artz, J.D., Amani, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

Crystal structure of Cryptosporidium parvum adenylate kinase cgd5_3360.

Wernimont, A.K., Lew, J., Kozieradzki, I., Lin, Y.H., Sun, X., Khuu, C., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bochkarev, A., Hui, R., Artz, J.D., Amani, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.98 kDa 
• Atom Count: 2,026 
• Modelled Residue Count: 215 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A	217	Cryptosporidium parvum Iowa II	Mutation(s): 0  Gene Names: cdg5_3360
UniProt
Find proteins for Q5CRC5 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CRC5  Go to UniProtKB:  Q5CRC5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP5	C [auth A]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C20 H29 N10 O22 P5 OIMACDRJUANHTJ-XPWFQUROSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.175	α = 90
b = 101.175	β = 90
c = 72.433	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Wernimont, A.K., Lew, J., Kozieradzki, I., Lin, Y.H., Sun, X., Khuu, C., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bochkarev, A., Hui, R., Artz, J.D., Amani, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2023-08-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description