5Y09 | pdb_00005y09

Crystal structure of Deg9 at 295 K

• PDB DOI: https://doi.org/10.2210/pdb5Y09/pdb

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


• Deposited: 2017-07-15 Released: 2017-10-18 
• Deposition Author(s): Ouyang, M., Li, X.Y., Liu, L., Zhang, L.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.253 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Deg9 at 295 K

Ouyang, M., Li, X.Y., Zhao, S., Zhang, L.X.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 124.76 kDa 
• Atom Count: 6,685 
• Modeled Residue Count: 834 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease Do-like 9	A, B	566	Arabidopsis thaliana	Mutation(s): 0  Gene Names: Deg9, DEGP9, At5g40200, MSN9.10, MSN9.100 EC: 3.4.21
UniProt
Find proteins for Q9FL12 (Arabidopsis thaliana) Explore Q9FL12  Go to UniProtKB:  Q9FL12

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.253 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.372	α = 90
b = 132.372	β = 90
c = 154.73	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Ouyang, M., Li, X.Y., Liu, L., Zhang, L.X.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description