6XAF | pdb_00006xaf

1.9A crystal structure of the GTPase domain of Parkinson's disease-associated protein LRRK2 carrying R1398H

• PDB DOI: https://doi.org/10.2210/pdb6XAF/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-06-04 Released: 2021-06-09 
• Deposition Author(s): Hoang, Q.Q., Liao, J., Huang, X., Park, Y., Wu, C.X.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structural basis for conformational plasticity in the GTPase domain of the Parkinson's disease-associated protein LRRK2

Wu, C.X., Liao, J., Park, Y., Hoang, N.C., Engel, V.A., Sanishvili, R., Takagi, Y., Johnson, S.M., Wang, M., Federici, M., Nichols, R.J., Cookson, M.R., Hoang, Q.Q.

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: 47.69 kDa 
• Atom Count: 2,901 
• Modeled Residue Count: 346 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat serine/threonine-protein kinase 2	A, B	206	Homo sapiens	Mutation(s): 3  Gene Names: LRRK2, PARK8 EC: 2.7.11.1 (PDB Primary Data), 3.6.5 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5S007 (Homo sapiens) Explore Q5S007  Go to UniProtKB:  Q5S007
PHAROS:  Q5S007 GTEx:  ENSG00000188906

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.497	α = 90
b = 101.785	β = 101.38
c = 44.527	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Hoang, Q.Q., Liao, J., Huang, X., Park, Y., Wu, C.X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM111639
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115844

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description