6HYB | pdb_00006hyb

Zr(IV)-substituted Wells-Dawson binding to Hen Egg-White Lysozyme (HEWL)

• PDB DOI: https://doi.org/10.2210/pdb6HYB/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2018-10-19 Released: 2019-10-30 
• Deposition Author(s): Vandebroek, L., Van Meervelt, L., Parac-Vogt, T.N.
• Funding Organization(s): Research Foundation - Flanders

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Noncovalent Complexes Formed between Metal-Substituted Polyoxometalates and Hen Egg White Lysozyme

Vandebroek, L., Mampaey, Y., Antonyuk, S., Van Meervelt, L., Parac-Vogt, T.N.

(2019) Eur J Inorg Chem 

• DOI: https://doi.org/10.1002/ejic.201801113

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.51 kDa 
• Atom Count: 1,134 
• Modeled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	128	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZRW (Subject of Investigation/LOI)	B [auth A]	W-Zr-cluster H2 O61 P2 W17 Zr LRQWFSUELMUBNO-UHFFFAOYSA-M
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.61	α = 90
b = 78.61	β = 90
c = 37.11	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Vandebroek, L., Van Meervelt, L., Parac-Vogt, T.N.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	--

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary