6C86

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine

• PDB DOI: https://doi.org/10.2210/pdb6C86/pdb

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


• Deposited: 2018-01-24 Released: 2018-02-28 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.204 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine

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 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 124.46 kDa 
• Atom Count: 8,980 
• Modelled Residue Count: 998 
• Deposited Residue Count: 1,070 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B	535	Cryptosporidium parvum Iowa II	Mutation(s): 0  Gene Names: cgd4_2370 EC: 6.1.1.6
UniProt
Find proteins for Q5CR27 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CR27  Go to UniProtKB:  Q5CR27

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KAA (Subject of Investigation/LOI)	C [auth A], G [auth B]	5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE C16 H26 N8 O7 S NARKTLKJPPMFJF-LEJQEAHTSA-N
SO4	F [auth A], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.204 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M36C86

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.03	α = 90
b = 142.87	β = 90
c = 73.24	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description