5F9Z | pdb_00005f9z

Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with Halofuginone and AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb5F9Z/pdb

• Classification: LIGASE
• Organism(s): Cryptosporidium parvum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-10 Released: 2016-11-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with Halofuginone and AMPPNP

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Dranow, D.M., Fox III, D., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

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: 120.74 kDa 
• Atom Count: 8,307 
• Modeled Residue Count: 981 
• Deposited Residue Count: 1,022 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoacyl-tRNA synthetase	A, B	511	Cryptosporidium parvum	Mutation(s): 0  Gene Names: 1MB.635

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A], H [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
HFG	E [auth A], I [auth B]	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one C16 H17 Br Cl N3 O3 LVASCWIMLIKXLA-CABCVRRESA-N
GOL	K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	F [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35F9Z

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.4	α = 90
b = 108.72	β = 90
c = 126.35	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description