7L3O | pdb_00007l3o

Crystal Structure of the RNA binding domain of Threonyl-tRNA synthetase from Cryptosporidium parvum Iowa II

• PDB DOI: https://doi.org/10.2210/pdb7L3O/pdb

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


• Deposited: 2020-12-18 Released: 2020-12-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the RNA binding domain of Threonyl-tRNA synthetase from Cryptosporidium parvum Iowa II

Abendroth, J., Dranow, D.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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: 205.96 kDa 
• Atom Count: 13,845 
• Modeled Residue Count: 1,602 
• Deposited Residue Count: 1,768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonyl-tRNA synthetase	A, B, C, D	442	Cryptosporidium parvum Iowa II	Mutation(s): 0  Gene Names: cgd7_1710 EC: 6.1.1.3
UniProt
Find proteins for Q5CYN0 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CYN0  Go to UniProtKB:  Q5CYN0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], G [auth B], I [auth C], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37l3o

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.73	α = 91.585
b = 67.45	β = 97.53
c = 143.18	γ = 120.777

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-12-30
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description