8P5Q

Structure of an ALOG domain from Arabidopsis thaliana in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb8P5Q/pdb
• NAKB: 8P5Q

• Classification: DNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-24 Released: 2024-02-21 
• Deposition Author(s): Zubieta, C., Nanao, M.H., Rieu, P.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.252 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Structure of an ALOG domain from Arabidopsis thaliana in complex with DNA

Rieu, P., Lucas, J., Thevenon, E., Dumas, R., Beretta, V., Caselli, F., Franchini, E., Caporali, E., Kater, M., Zubieta, C., Nanao, M.H., Gregis, V., Parcy, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 25.58 kDa 
• Atom Count: 1,809 
• Modelled Residue Count: 163 
• Deposited Residue Count: 163 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 3	A	129	Arabidopsis thaliana	Mutation(s): 0  Gene Names: LSH3, OBO1, At2g31160, T16B12.3
UniProt
Find proteins for O82268 (Arabidopsis thaliana) Explore O82268  Go to UniProtKB:  O82268

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*GP*TP*CP*AP*AP*CP*AP*GP*TP*AP*AP*AP*CP*TP*A)-3')	B	17	Arabidopsis thaliana

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*TP*TP*TP*AP*CP*TP*GP*TP*TP*GP*AP*CP*GP*T)-3')	C	17	Arabidopsis thaliana

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.252 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.798	α = 90
b = 79.798	β = 90
c = 127.012	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Zubieta, C., Nanao, M.H., Rieu, P.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release