4LV5 | pdb_00004lv5

Murine IRGa6 bound to Toxoplasma ROP5B, a pseudokinase GDI

• PDB DOI: https://doi.org/10.2210/pdb4LV5/pdb

• Classification: Transferase/Hydrolase
• Organism(s): Toxoplasma gondii, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-25 Released: 2013-09-25 
• Deposition Author(s): Reese, M.L., Boothroyd, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Models: experimental

Literature

Murine IRGa6 bound to Toxoplasma ROP5B, a pseudokinase GDI

Reese, M.L., Shah, N., Boothroyd, J.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.02 kDa 
• Atom Count: 6,642 
• Modeled Residue Count: 746 
• Deposited Residue Count: 794 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhoptry protein 5B	A	371	Toxoplasma gondii	Mutation(s): 0  Gene Names: ROP5, ROP5B
UniProt
Find proteins for F2YGR7 (Toxoplasma gondii) Explore F2YGR7  Go to UniProtKB:  F2YGR7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-inducible GTPase 1	B	423	Mus musculus	Mutation(s): 0  Gene Names: Iigp1, Irga6 EC: 3.6.5
UniProt
Find proteins for Q9QZ85 (Mus musculus) Explore Q9QZ85  Go to UniProtKB:  Q9QZ85

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	I [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BME	D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.6	α = 99
b = 54.7	β = 106.6
c = 85.6	γ = 106.9

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Reese, M.L., Boothroyd, J.C.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Derived calculations
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description