3WYH | pdb_00003wyh

Structure of disulfide bond deletion mutant of ostrich egg white lysozyme

• PDB DOI: https://doi.org/10.2210/pdb3WYH/pdb

• Classification: HYDROLASE
• Organism(s): Struthio camelus
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2014-08-28 Released: 2014-10-15 
• Deposition Author(s): Kawaguchi, Y., Yoneda, K., Araki, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.224 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Structure of disulfide bond deletion mutant of ostrich egg white lysozyme

Kawaguchi, Y., Yoneda, K., Araki, 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)

Macromolecule Content 

• Total Structure Weight: 41.68 kDa 
• Atom Count: 3,200 
• Modeled Residue Count: 370 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme g	A, B	185	Struthio camelus	Mutation(s): 4  EC: 3.2.1.17
UniProt
Find proteins for P00719 (Struthio camelus) Explore P00719  Go to UniProtKB:  P00719

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
TAM	C [auth A], E [auth B]	TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.224 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.188	α = 90
b = 64.934	β = 90
c = 131.118	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Kawaguchi, Y., Yoneda, K., Araki, T.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description