6G5C | pdb_00006g5c

Interaction of TiO2 nanoparticles (NM-101) with Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb6G5C/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Peptide display vector fth1
• Mutation(s): No 


• Deposited: 2018-03-29 Released: 2018-10-24 
• Deposition Author(s): Sbirkova-Dimitrova, H.I., Radoslavov, G., Hristov, P., Ganev, V., Dimowa, L., Rusev, R., Shivachev, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.204 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystallization and crystal structure of lysozyme in the presence of nanosized Titanium dioxide

Shivachev, B.L., Sbirkova-Dimitrova, H.I.

(2018) Bulg Chem Commun 50

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis, mass spectrometry

Macromolecule Content 

• Total Structure Weight: 14.69 kDa 
• Atom Count: 1,120 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
4TI (Subject of Investigation/LOI)	H [auth A]	TITANIUM ION Ti VEOOXLFYKHRLHJ-UHFFFAOYSA-N
CL	I [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], E [auth A], F [auth A], G [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.204 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.866	α = 90
b = 78.866	β = 90
c = 36.893	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Sbirkova-Dimitrova, H.I., Radoslavov, G., Hristov, P., Ganev, V., Dimowa, L., Rusev, R., Shivachev, B.L.

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Funding Organization	Location	Grant Number
	Bulgaria	NSFB T0214

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2019-03-13
  Changes: Data collection, Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary