9U3O | pdb_00009u3o

Crystal structure of Chi430 mutant E176A in the substrate complex

• PDB DOI: https://doi.org/10.2210/pdb9U3O/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-03-18 Released: 2025-08-06 
• Deposition Author(s): Qipeng, C., Jinghan, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.203 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Chi430 mutant E173A in the substrate complex

Qipeng, C., Jinghan, Z.

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

Macromolecule Content 

• Total Structure Weight: 46.85 kDa 
• Atom Count: 3,505 
• Modeled Residue Count: 410 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chitinase	A	411	Vibrio parahaemolyticus	Mutation(s): 1  Gene Names: HKB16_33210 EC: 3.2.1.14
UniProt
Find proteins for A0A7Y0XG39 (Vibrio parahaemolyticus) Explore A0A7Y0XG39  Go to UniProtKB:  A0A7Y0XG39

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan: G01361SX GlyCosmos: G01361SX GlyGen: G01361SX

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.203 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.676	α = 90
b = 49.858	β = 125.62
c = 92.602	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Qipeng, C., Jinghan, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32202987

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release
  
• Version 2.0: 2025-10-15
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary