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

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of CsChiL, a chitinase from Chitiniphilus shinanonensis

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

To be published.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8WSX2
Sequence Annotations Expand
Reference Sequence

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	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B]	N [auth A], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth A] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain X [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	R [auth B], S [auth B], T [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain U [auth B] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B]	J [auth A], U [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain J [auth A] Focus chain U [auth B]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B]
MXE Query on MXE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-METHOXYETHANOL C₃ H₈ O₂ XNWFRZJHXBZDAG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	K [auth A], L [auth A], M [auth A], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain V [auth B] Focus chain W [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B]	E [auth A], O [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain O [auth B]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Ueda, M.

Shimosaka, M.

Arai, R.

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 (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary