2XJW

Lysozyme-CO releasing molecule adduct

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 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RU
Query on RU
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO
Query on CMO
Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
M [auth A]
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
Query on NA
Download Ideal Coordinates CCD File 
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 = 78.4α = 90
b = 78.4β = 90
c = 36.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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