5YLG | pdb_00005ylg

Crystal Structure of LysM domain from pteris ryukyuensis chitinase A

• PDB DOI: https://doi.org/10.2210/pdb5YLG/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pteris ryukyuensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-17 Released: 2018-10-24 
• Deposition Author(s): Ohnuma, T., Kitaoku, Y., Umemoto, N., Numata, T., Fukamizo, T.
• Funding Organization(s): MEXT (Ministry of Education, Culture, Sports, Science, and Technology)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.220 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of LysM domain from pteris ryukyuensis chitinase A

Kitaoku, Y., Umemoto, N., Taira, T., Fukamizo, T., Numata, T., Ohnuma, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.5 kDa 
• Atom Count: 1,590 
• Modeled Residue Count: 188 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase A	A, B, C, D	49	Pteris ryukyuensis	Mutation(s): 0  Gene Names: prchiA
UniProt
Find proteins for Q0WYK2 (Pteris ryukyuensis) Explore Q0WYK2  Go to UniProtKB:  Q0WYK2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], I [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.220 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.839	α = 90
b = 50.125	β = 90
c = 92.362	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
Coot	model building
PHASER	phasing
DENZO	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Ohnuma, T., Kitaoku, Y., Umemoto, N., Numata, T., Fukamizo, T.

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Funding Organization	Location	Grant Number
MEXT (Ministry of Education, Culture, Sports, Science, and Technology)	Japan	S1101035

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary