2XJW

Lysozyme-CO releasing molecule adduct

• PDB DOI: https://doi.org/10.2210/pdb2XJW/pdb

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


• Deposited: 2010-07-06 Released: 2011-01-26 
• Deposition Author(s): Santos-Silva, T., Mukhopadhyay, A., Romao, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.208 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Corm-3 Reactivity Toward Proteins: The Crystal Structure of a Ru(II) Dicarbonyl-Lysozyme Complex.

Santos-Silva, T., Mukhopadhyay, A., Seixas, J.D., Bernardes, G.J., Romao, C.C., Romao, M.J.

(2011) J Am Chem Soc 133: 1192

• PubMed: 21204537 
• DOI: https://doi.org/10.1021/ja108820s
• Primary Citation of Related Structures:  
  2XJW


• PubMed Abstract: 
  

  CORM-3, [fac-Ru(CO)(3)Cl(κ(2)-H(2)NCH(2)CO(2))], is a well-known carbon monoxide releasing molecule (CORM) capable of delivering CO in vivo. Herein we show for the first time that the interactions of CORM-3 with proteins result in the loss of a chloride ion, glycinate, and one CO ligand. The rapid formation of stable adducts between the protein and the remaining cis-Ru(II)(CO)(2) fragments was confirmed by Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES), Liquid-Chromatography Mass Spectrometry (LC-MS), Infrared Spectroscopy (IR), and X-ray crystallography. Three Ru coordination sites are observed in the structure of hen egg white lysozyme crystals soaked with CORM-3. The site with highest Ru occupancy (80%) shows a fac-[(His15)Ru(CO)(2)(H(2)O)(3)] structure.

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Organizational Affiliation: 

REQUIMTE-CQFB, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 14.93 kDa 
• Atom Count: 1,194 
• Modelled 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RU	B [auth A], C [auth A], D [auth A]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N
CL	J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO	F [auth A], G [auth A], H [auth A], I [auth A], M [auth A], N [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.208 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.4	α = 90
b = 78.4	β = 90
c = 36.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Santos-Silva, T., Mukhopadhyay, A., Romao, M.J.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-19
  Changes: Database references, Structure summary
• Version 1.4: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 1.5: 2019-11-27
  Changes: Derived calculations, Other
• Version 1.6: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.7: 2024-10-23
  Changes: Structure summary