9YRU | pdb_00009yru

Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form)

• PDB DOI: https://doi.org/10.2210/pdb9YRU/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-17 Released: 2025-10-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 
  0.288 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form)

Liu, L., Lovell, S., Battaile, K.P.

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

Macromolecule Content 

• Total Structure Weight: 109.2 kDa 
• Atom Count: 6,523 
• Modeled Residue Count: 840 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine--tRNA ligase	A, B	466	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF3D7_1015200.1 EC: 6.1.1.16
UniProt
Find proteins for Q8IJP3 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJP3  Go to UniProtKB:  Q8IJP3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free:  0.288 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39YRU

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.874	α = 90
b = 104.024	β = 90
c = 158.805	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release