6KXL

Crystal structure of the catalytic domain of Chitiniphilus shinanonensis chitinase ChiL (CsChiL) complexed with N,N'-diacetylchitobiose

• PDB DOI: https://doi.org/10.2210/pdb6KXL/pdb

• Classification: HYDROLASE
• Organism(s): Chitiniphilus shinanonensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-12 Released: 2020-09-16 
• Deposition Author(s): Ueda, M., Shimosaka, M., Arai, R.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.148 
• R-Value Work: 0.118 
• R-Value Observed: 0.120 

Literature

Crystal structure of CsChiL, a chitinase from Chitiniphilus shinanonensis

Ueda, M., Sonoda, N., Shimosaka, M., Arai, R.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.96 kDa 
• Atom Count: 7,354 
• Modelled Residue Count: 735 
• Deposited Residue Count: 744 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Family 18 chitinase	A, B	372	Chitiniphilus shinanonensis	Mutation(s): 0  Gene Names: chiL
UniProt
Find proteins for F8WSX2 (Chitiniphilus shinanonensis) Explore F8WSX2  Go to UniProtKB:  F8WSX2

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	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	N [auth A], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	R [auth B], S [auth B], T [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	J [auth A], U [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MLI	G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
MXE	F [auth A]	2-METHOXYETHANOL C3 H8 O2 XNWFRZJHXBZDAG-UHFFFAOYSA-N
EDO	K [auth A], L [auth A], M [auth A], V [auth B], W [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth A], O [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.148 
• R-Value Work: 0.118 
• R-Value Observed: 0.120 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.982	α = 90
b = 82.502	β = 90
c = 131.818	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Ueda, M., Shimosaka, M., Arai, R.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP24780097
Japan Society for the Promotion of Science	Japan	JP24580107
Japan Society for the Promotion of Science	Japan	JP24113707
Japan Society for the Promotion of Science	Japan	JP16K05841
Japan Society for the Promotion of Science	Japan	JP16H00761
Japan Society for the Promotion of Science	Japan	JP17KK0104
Japan Society for the Promotion of Science	Japan	JP19H02522

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description