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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.189 (Depositor), 0.188 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Peptide asparaginyl ligase from Viola canadensis

Wong, Y.H., Lescar, J.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A384E113
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.189 (Depositor), 0.188 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.