3WIJ

Crystal structure of a plant class V chitinase mutant from Cycas revoluta in complex with (GlcNAc)3

• PDB DOI: https://doi.org/10.2210/pdb3WIJ/pdb

• Classification: HYDROLASE
• Organism(s): Cycas revoluta
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-09-13 Released: 2014-09-17 
• Deposition Author(s): Numata, T., Osawa, T., Umemoto, N., Ohnuma, T., Fukamizo, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.197 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Crystal structure of a plant class V chitinase mutant from Cycas revoluta in complex with (GlcNAc)3

Numata, T., Osawa, T., Umemoto, N., Ohnuma, T., Fukamizo, T.

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: 39.63 kDa 
• Atom Count: 2,972 
• Modelled Residue Count: 340 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase A	A	348	Cycas revoluta	Mutation(s): 1  Gene Names: crchiA EC: 3.2.1.14
UniProt
Find proteins for Q4W6L6 (Cycas revoluta) Explore Q4W6L6  Go to UniProtKB:  Q4W6L6

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	B	3		N/A
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	C [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
ACT	D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	B	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.197 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.651	α = 90
b = 63.916	β = 90
c = 86.048	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Numata, T., Osawa, T., Umemoto, N., Ohnuma, T., Fukamizo, T.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary