5V4I

Osmium(II)(cymene)(chlorido)2-lysozyme adduct with one binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The metalation of hen egg white lysozyme impacts protein stability as shown by ion mobility mass spectrometry, differential scanning calorimetry, and X-ray crystallography.

Sullivan, M.P.Groessl, M.Meier, S.M.Kingston, R.L.Goldstone, D.C.Hartinger, C.G.

(2017) Chem Commun (Camb) 53: 4246-4249

  • DOI: https://doi.org/10.1039/c6cc10150j
  • Primary Citation of Related Structures:  
    5V4G, 5V4H, 5V4I

  • PubMed Abstract: 

    Metalation of hen egg white lysozyme (HEWL) with organometallics was studied with physicochemical methods in solid state, solution and the gas phase. While metalation did not affect the crystal structure of HEWL significantly, protein destabilisation was detected in gas phase and solution.


  • Organizational Affiliation

    School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. c.hartinger@auckland.ac.nz.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8WV
Query on 8WV

Download Ideal Coordinates CCD File 
C [auth A]dichloro[(1,2,3,4,5,6-eta)-3-methyl-6-(propan-2-yl)benzene-1,2,4,5-tetrayl]osmium
C10 H10 Cl2 Os
WKSPPTHHDBHBPQ-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.594α = 90
b = 80.594β = 90
c = 36.987γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-04-19
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary