Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 15676.52 
• Atom Count: 1033 
• Residue Count: 129 
• Unique protein chains: 1

4W96

Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked with 5mM [Ru(CO)3Cl2]2 followed by the reaction in deoxy-myoglobin solution

• DOI: 10.2210/pdb4W96/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Gallus gallus


• Deposited: 2014-08-27 Released: 2014-12-31 
• Deposition Author(s): Tabe, H., Fujita, K., Abe, S., Tsujimoto, M., Kuchimaru, T., Kizaka-Kondo, S., Takano, M., Kitagawa, S., Ueno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.227 
• R-Value Work: 0.195 

Literature

Preparation of a Cross-Linked Porous Protein Crystal Containing Ru Carbonyl Complexes as a CO-Releasing Extracellular Scaffold

Tabe, H., Fujita, K., Abe, S., Tsujimoto, M., Kuchimaru, T., Kizaka-Kondoh, S., Takano, M., Kitagawa, S., Ueno, T.

(2015) Inorg.Chem. 54: 215-220

• PubMed: 25494847 
• DOI: 10.1021/ic502159x
• Primary Citation of Related Structures:  
  4W94


• PubMed Abstract: 
  

Protein crystals generally are stable solid protein assemblies. Certain protein crystals are suitable for use as nanovessels for immobilizing metal complexes. Here we report the preparation of ruthenium carbonyl-incorporated cross-linked hen egg white lysozyme crystals (Ru·CL-HEWL). Ru·CL-HEWL retains a Ru carbonyl moiety that can release CO, although a composite of Ru carbonyl-HEWL dissolved in buffer solution (Ru·HEWL) does not release CO. We found that treatment of cells with Ru·CL-HEWL significantly increased nuclear factor kappa B (NF-κB) activity as a cellular response to CO. These results demonstrate that Ru·CL-HEWL has potential for use as an artificial extracellular scaffold suitable for transport and release of a gas molecule.

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Organizational Affiliation: 

Graduate School of Engineering, Kyoto University, Katsura , Nishikyo-ku, Kyoto 615-8510, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Go to Gene View: LYZ Go to UniProtKB:  P00698

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
RU	A	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
DMF	A	DIMETHYLFORMAMIDE C3 H7 N O ZMXDDKWLCZADIW-UHFFFAOYSA-N
RU1	A	bis(oxidaniumylidynemethyl)ruthenium(2+) C2 O2 Ru HLYOBVRGNSSECA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.227 
• R-Value Work: 0.195 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 79.011	α = 90.00
b = 79.011	β = 90.00
c = 36.994	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data reduction
MOLREP	phasing
MOLREP	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
DENZO	data collection
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-27 
• Released Date: 2014-12-31 
• Deposition Author(s): Tabe, H., Fujita, K., Abe, S., Tsujimoto, M., Kuchimaru, T., Kizaka-Kondo, S., Takano, M., Kitagawa, S., Ueno, T.

Revision History 

• Version 1.0: 2014-12-31
  Type: Initial release
• Version 1.1: 2015-01-14
  Type: Database references
• Version 1.2: 2020-01-29
  Type: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy