4J7V | pdb_00004j7v

Crystal structure of cross-linked hen egg white lysozyme soaked with 5mM [Ru(benzene)Cl2]2

• PDB DOI: https://doi.org/10.2210/pdb4J7V/pdb

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


• Deposited: 2013-02-14 Released: 2014-02-19 
• Deposition Author(s): Tabe, H., Abe, S., Hikage, T., Kitagawa, S., Ueno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Porous protein crystals as catalytic vessels for organometallic complexes.

Tabe, H., Abe, S., Hikage, T., Kitagawa, S., Ueno, T.

(2014) Chem Asian J 9: 1373-1378

• PubMed: 24677803 
• DOI: https://doi.org/10.1002/asia.201301347
• Primary Citation Related Structures: 
  3W6A, 4J7V


• PubMed Abstract: 
  

  Porous protein crystals, which are protein assemblies in the solid state, have been engineered to form catalytic vessels by the incorporation of organometallic complexes. Ruthenium complexes in cross-linked porous hen egg white lysozyme (HEWL) crystals catalyzed the enantioselective hydrogen-transfer reduction of acetophenone derivatives. The crystals accelerated the catalytic reaction and gave different enantiomers based on the crystal form (tetragonal or orthorhombic). This method represents a new approach for the construction of bioinorganic catalysts from protein crystals.

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Organizational Affiliation: 
• Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510 (Japan); Institute for Integrated Cell-Material Sciences), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan).

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: 14.78 kDa 
• Atom Count: 1,107 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RBN	H [auth A]	Benzeneruthenium(II) chloride C6 H6 Cl2 Ru NDWWOISDNSYBCH-UHFFFAOYSA-L
CL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.194	α = 90
b = 55.572	β = 90
c = 72.418	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Tabe, H., Abe, S., Hikage, T., Kitagawa, S., Ueno, T.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2024-11-20
  Changes: Database references