6DKN | pdb_00006dkn

CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA DECAPPING NUCLEASE DXO1

• PDB DOI: https://doi.org/10.2210/pdb6DKN/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-30 Released: 2019-02-27 
• Deposition Author(s): Tong, L., Wang, V.Y.F.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Arabidopsis DXO1 links RNA turnover and chloroplast function independently of its enzymatic activity.

Kwasnik, A., Wang, V.Y., Krzyszton, M., Gozdek, A., Zakrzewska-Placzek, M., Stepniak, K., Poznanski, J., Tong, L., Kufel, J.

(2019) Nucleic Acids Res 47: 4910-4910

• PubMed: 30949693 
• DOI: https://doi.org/10.1093/nar/gkz257
• Primary Citation Related Structures: 
  6DKN

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Organizational Affiliation: 
• Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 80.65 kDa 
• Atom Count: 5,941 
• Modeled Residue Count: 672 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decapping nuclease DXO homolog, chloroplastic	A, B	349	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At4g17620, dl4845w, FCAALL.74 EC: 3.6.1
UniProt
Find proteins for Q8RY73 (Arabidopsis thaliana) Explore Q8RY73  Go to UniProtKB:  Q8RY73

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.08	α = 90
b = 80.878	β = 90
c = 125.88	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Tong, L., Wang, V.Y.F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R35GM118093
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2019-05-22
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description