5LXU | pdb_00005lxu

Structure of the DNA-binding domain of LUX ARRHYTHMO

• PDB DOI: https://doi.org/10.2210/pdb5LXU/pdb
• NAKB: 5LXU

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


• Deposited: 2016-09-22 Released: 2017-10-25 
• Deposition Author(s): Zubieta, C., Nanao, M.H.
• Funding Organization(s): ATIP-Avenir

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.232 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Structure of the DNA-binding domain of LUX ARRHYTHMO

Zubieta, C., Silva, C.S., Lai, X., Wigge, P., Nanao, M.H., Nayak, A.

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)

Macromolecule Content 

• Total Structure Weight: 12.9 kDa 
• Atom Count: 968 
• Modeled Residue Count: 77 
• Deposited Residue Count: 77 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor LUX	A	57	Arabidopsis thaliana	Mutation(s): 0  Gene Names: LUX, PCL1, At3g46640, F12A12.160
UniProt
Find proteins for Q9SNB4 (Arabidopsis thaliana) Explore Q9SNB4  Go to UniProtKB:  Q9SNB4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')	B [auth U]	10	Arabidopsis thaliana

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')	C [auth B]	10	Arabidopsis thaliana

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.232 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.16	α = 90
b = 32.83	β = 98.61
c = 53.76	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SHELX	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Zubieta, C., Nanao, M.H.

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Funding Organization	Location	Grant Number
ATIP-Avenir	France	--

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary