5Z34 | pdb_00005z34

The structure of a chitin deacetylase from Bombyx mori provide the first insight into insect chitin deacetylation mechanism

• PDB DOI: https://doi.org/10.2210/pdb5Z34/pdb

• Classification: HYDROLASE
• Organism(s): Bombyx mori
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2018-01-05 Released: 2019-02-20 
• Deposition Author(s): Liu, L., Zhou, Y., Yang, Q.
• Funding Organization(s): National Natural Science Funds for Distinguished Young Scholar

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

The structure of a chitin deacetylase from Bombyx mori provide the first insight into insect chitin deacetylation mechanism

Liu, L., Zhou, Y., Yang, Q.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 42.82 kDa 
• Atom Count: 3,096 
• Modeled Residue Count: 361 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitin deacetylase	A	369	Bombyx mori	Mutation(s): 0  EC: 3.5.1.41
UniProt
Find proteins for H9JW43 (Bombyx mori) Explore H9JW43  Go to UniProtKB:  H9JW43
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.017	α = 90
b = 115.017	β = 90
c = 106.51	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHENIX	phasing
Coot	model building
HKL-3000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Liu, L., Zhou, Y., Yang, Q.

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Funding Organization	Location	Grant Number
National Natural Science Funds for Distinguished Young Scholar	China	31425021

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary