5DHD | pdb_00005dhd

Crystal structure of ChBD2 from Thermococcus kodakarensis KOD1

• PDB DOI: https://doi.org/10.2210/pdb5DHD/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-30 Released: 2016-02-10 
• Deposition Author(s): Hibi, M., Niwa, S., Takeda, K., Miki, K.
• Funding Organization(s): CREST, JST

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.195 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.214 (DCC) 

Starting Model: experimental

Literature

Crystal structures of chitin binding domains of chitinase from Thermococcus kodakarensis KOD1

Hanazono, Y., Takeda, K., Niwa, S., Hibi, M., Takahashi, N., Kanai, T., Atomi, H., Miki, K.

(2016) FEBS Lett 590: 298-304

• PubMed: 26823175 
• DOI: https://doi.org/10.1002/1873-3468.12055
• Primary Citation Related Structures: 
  5DHD, 5DHE


• PubMed Abstract: 
  

  Chitinase from T. kodakarensis (TkChiA) catalyzes the hydrolysis of chitin. The enzyme consists of two catalytic and three binding domains (ChBD1, ChBD2 and ChBD3). ChBD2 and ChBD3 can bind to not only chitin but also cellulose. In both domains, the intervals of the side chains of the three tryptophan residues, which are located on the molecular surface, correspond to twice the length of the lattice of the chitin. A binding model with crystalline chitin implies that the tryptophan residues and a glutamate residue interact with the hexose ring by CH-π interactions and the amide group by a hydrogen bond, respectively.

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Japan.
Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Japan.
CREST/JST, Chiyoda-ku, Tokyo, Japan.

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: 14.93 kDa 
• Atom Count: 959 
• Modeled Residue Count: 98 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase	A	100	Thermococcus kodakarensis KOD1	Mutation(s): 0  Gene Names: Pk-chiA, TK1765 EC: 3.2.1.14
UniProt
Find proteins for Q9UWR7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q9UWR7  Go to UniProtKB:  Q9UWR7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.195 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.214 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.245	α = 90
b = 60.245	β = 90
c = 68.845	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data collection
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Hibi, M., Niwa, S., Takeda, K., Miki, K.

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Funding Organization	Location	Grant Number
CREST, JST	Japan	--

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description