5ZBI | pdb_00005zbi

Crystal structure of asparaginyl endopeptidases from Viola Canadensis

• PDB DOI: https://doi.org/10.2210/pdb5ZBI/pdb

• Classification: PLANT PROTEIN
• Organism(s): Viola canadensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-12 Released: 2018-05-09 
• Deposition Author(s): Wong, Y.H., Lescar, J.
• Funding Organization(s): Ministry of Education (Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Peptide asparaginyl ligase from Viola canadensis

Wong, Y.H., Lescar, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
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: 119.09 kDa 
• Atom Count: 7,056 
• Modeled Residue Count: 835 
• Deposited Residue Count: 1,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide asparaginyl ligase	A, B	532	Viola canadensis	Mutation(s): 0
UniProt
Find proteins for A0A384E113 (Viola canadensis) Explore A0A384E113  Go to UniProtKB:  A0A384E113

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.47	α = 90
b = 62.08	β = 106.81
c = 82.91	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Wong, Y.H., Lescar, J.

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Funding Organization	Location	Grant Number
Ministry of Education (Singapore)	Singapore	MOE2016-T3-1-003

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary