5V4H | pdb_00005v4h

Ruthenium(II)(cymene)(chlorido)2-lysozyme adduct formed when ruthenium(II)(cymene)(bromido)2 underwent ligand exchange, resulting in one binding site

• PDB DOI: https://doi.org/10.2210/pdb5V4H/pdb

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


• Deposited: 2017-03-09 Released: 2017-04-05 
• Deposition Author(s): Sullivan, M.P., Hartinger, C.G., Goldstone, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

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

• PubMed: 28361137 
• DOI: https://doi.org/10.1039/c6cc10150j
• Primary Citation 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.

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Organizational Affiliation: 
• School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. [e-mail].

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: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 14.66 kDa 
• Atom Count: 1,163 
• 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  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
RU7	C [auth A]	PARA-CYMENE RUTHENIUM CHLORIDE C10 H14 Cl2 Ru UCXDWSTYBSBFFB-UHFFFAOYSA-L
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.32	α = 90
b = 80.32	β = 90
c = 36.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Sullivan, M.P., Hartinger, C.G., Goldstone, D.C.

Revision History  

• 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, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary