6G5C

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.204
R-Value Work: 0.166
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
4TI (Subject of Investigation/LOI) Query on 4TI Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	TITANIUM ION Ti VEOOXLFYKHRLHJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A]	I [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain K [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.204
R-Value Work: 0.166
R-Value Observed: 0.167
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Sbirkova-Dimitrova, H.I.

Funding Organization	Location	Grant Number
	Bulgaria	NSFB T0214

Revision History (Full details and data files)

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