7PVF | pdb_00007pvf

Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 3-hydroxy-1lambda6-thietane-1,1-dione

• PDB DOI: https://doi.org/10.2210/pdb7PVF/pdb

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


• Deposited: 2021-10-02 Released: 2022-10-05 
• Deposition Author(s): Duclovel, C., Gelin, M., Krimm, I., Cerdan, R., Guichou, J.-F.
• Funding Organization(s): French Infrastructure for Integrated Structural Biology (FRISBI), Montpellier University of Excellence (MUSE)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design of PfCCT inhibitors

Duclovel, C., Gelin, M., Wein, S., Wengelnik, K., Krimm, I., Guichou, J.F., Cerdan, R.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.11 kDa 
• Atom Count: 1,108 
• Modeled Residue Count: 132 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinephosphate cytidylyltransferase	A	180	Plasmodium falciparum	Mutation(s): 0  Gene Names: ctP, MAL13P1.86 EC: 2.7.7.15
UniProt
Find proteins for Q8IEE9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IEE9  Go to UniProtKB:  Q8IEE9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HV2 (Subject of Investigation/LOI)	B [auth A], C [auth A]	1,1-bis(oxidanylidene)thietan-3-ol C3 H6 O3 S CIUZABLJPXPIFC-UHFFFAOYSA-N
GZ6 (Subject of Investigation/LOI)	D [auth A]	Guanidinium C H6 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.68	α = 90
b = 69.279	β = 90
c = 118.081	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Duclovel, C., Gelin, M., Krimm, I., Cerdan, R., Guichou, J.-F.

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Funding Organization	Location	Grant Number
French Infrastructure for Integrated Structural Biology (FRISBI)	France	--
Montpellier University of Excellence (MUSE)	France	--

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2022-10-26
  Changes: Derived calculations
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description