6KST | pdb_00006kst

Crystal structure of the catalytic domain of chitinase ChiL from Chitiniphilus shinanonensis (CsChiL)

PDB DOI: https://doi.org/10.2210/pdb6KST/pdb

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

Deposited: 2019-08-26 Released: 2020-08-26
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: 1.25 Å
R-Value Free:
0.161 (Depositor), 0.164 (DCC)
R-Value Work:
0.132 (Depositor), 0.141 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a chitinase (CsChiL) from Chitiniphilus shinanonensis

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

To be published.

Macromolecule Content

Total Structure Weight: 84.54 kDa
Atom Count: 7,635
Modeled Residue Count: 739
Deposited Residue Count: 744
Unique protein chains: 1

Macromolecules

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| 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 EC: 3.2.1.14
UniProt
Find proteins for F8WSX2 (Chitiniphilus shinanonensis) Explore F8WSX2 Go to UniProtKB: F8WSX2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F8WSX2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain W [auth B] SDF format, chain M [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth A] MOL2 format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth A] mmCIF format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain C [auth A]	C [auth A], L [auth A], M [auth A], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B]
MXE Query on MXE Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	N [auth B], O [auth B], P [auth B], Q [auth B]	2-METHOXYETHANOL C₃ H₈ O₂ XNWFRZJHXBZDAG-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	U [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.161 (Depositor), 0.164 (DCC)
R-Value Work: 0.132 (Depositor), 0.141 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.189	α = 90
b = 81.547	β = 90
c = 130.012	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-26

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		JP24580107
Japan Society for the Promotion of Science		JP24113707
Japan Society for the Promotion of Science		JP16K05841
Japan Society for the Promotion of Science		JP16H00761
Japan Society for the Promotion of Science		JP17KK0104
Japan Society for the Promotion of Science		JP19H02522

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary