8HW8

Crystal structure of Heterodera glycines chitinase 2 D129A/E131A mutant in complex with nodulation factor SmNF-V (C16:2, S)

• PDB DOI: https://doi.org/10.2210/pdb8HW8/pdb

• Classification: HYDROLASE
• Organism(s): Heterodera glycines
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2022-12-29 Released: 2024-06-05 
• Deposition Author(s): Chen, W., Chen, Q., Wang, D., Yang, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.187 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Crystal structure of Heterodera glycines chitinase 2 D129A/E131A mutant in complex with nodulation factor SmNF-V (C16:2, S)

Chen, W., Chen, Q., Wang, D., Yang, Q.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.13 kDa 
• Atom Count: 2,924 
• Modelled Residue Count: 326 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase	A	356	Heterodera glycines	Mutation(s): 2  EC: 3.2.1.14
UniProt
Find proteins for Q8I6X8 (Heterodera glycines) Explore Q8I6X8  Go to UniProtKB:  Q8I6X8
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-6-O-sulfo-beta-D-glucopyranose	B [auth D]	4		N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
68X (Subject of Investigation/LOI)	D [auth A]	(2~{Z},9~{E})-~{N}-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]hexadeca-2,9-dienamide C22 H39 N O6 BQDHAOHXPSOCQH-OQVMBZPUSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.187 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.005	α = 90
b = 69.384	β = 105.2
c = 50.818	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Chen, W., Chen, Q., Wang, D., Yang, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31830076
National Natural Science Foundation of China (NSFC)	China	32161133010
National Natural Science Foundation of China (NSFC)	China	32272595

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release