4PXV | pdb_00004pxv

Crystal Structure of LysM domain from pteris ryukyuensis chitinase A

• PDB DOI: https://doi.org/10.2210/pdb4PXV/pdb

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


• Deposited: 2014-03-25 Released: 2015-03-25 
• Deposition Author(s): Ohnuma, T., Umemoto, N., Numata, T., Fukamizo, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.229 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal Structure of LysM domain from pteris ryukyuensis chitinase A

Ohnuma, T., Numata, T., Taira, T., Fukamizo, T.

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 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.45 kDa 
• Atom Count: 1,550 
• Modeled Residue Count: 189 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.229 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.686	α = 90
b = 50.229	β = 90
c = 92.292	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SnB	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Ohnuma, T., Umemoto, N., Numata, T., Fukamizo, T.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary