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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1021/ic502159x
  • Primary Citation of Related Structures:  
    4W94, 4W96

  • 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) ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RU1
Query on RU1

Download Ideal Coordinates CCD File 
H [auth A]bis(oxidaniumylidynemethyl)ruthenium(2+)
C2 O2 Ru
HLYOBVRGNSSECA-UHFFFAOYSA-N
 Ligand Interaction
RU
Query on RU

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
N [auth A],
O [auth A],
P [auth A],
K [auth A],
L [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
S [auth A],
T [auth A]
RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
 Ligand Interaction
DMF
Query on DMF

Download Ideal Coordinates CCD File 
B [auth A]DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth A],
J [auth A],
M [auth A],
R [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.011α = 90
b = 79.011β = 90
c = 36.994γ = 90
Software Package:
Software NamePurpose
DENZOdata collection
SCALEPACKdata reduction
MOLREPdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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