8HRF | pdb_00008hrf

Catalytic domain of Vibrio parahaemolyticus chitinase 1

• PDB DOI: https://doi.org/10.2210/pdb8HRF/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-15 Released: 2023-12-20 
• Deposition Author(s): Nakamura, A.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: in silico

Literature

Catalytic domain of Vibrio parahaemolyticus chitinase 1

Nakamura, A.

To be published.

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: 124.19 kDa 
• Atom Count: 9,426 
• Modeled Residue Count: 1,136 
• Deposited Residue Count: 1,142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase	A, B	571	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: BS585_05230 EC: 3.2.1.14
UniProt
Find proteins for A0A9Q3UC14 (Vibrio parahaemolyticus) Explore A0A9Q3UC14  Go to UniProtKB:  A0A9Q3UC14

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth A], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.804	α = 90
b = 159.996	β = 92.68
c = 75.489	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Nakamura, A.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H03094

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary