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

PDB DOI: https://doi.org/10.2210/pdb4W96/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Expression System: Gallus gallus
Mutation(s): No

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.

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 1.3 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

PubMed: 25494847 Search on PubMed
DOI: https://doi.org/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). 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.

Macromolecule Content

Total Structure Weight: 15.68 kDa
Atom Count: 1,130
Modelled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RU1 Query on RU1 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	bis(oxidaniumylidynemethyl)ruthenium(2+) C₂ O₂ Ru HLYOBVRGNSSECA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
RU Query on RU Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	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		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A]
DMF Query on DMF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DIMETHYLFORMAMIDE C₃ H₇ N O ZMXDDKWLCZADIW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain R [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain R [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain R [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain R [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

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 = 79.011	α = 90
b = 79.011	β = 90
c = 36.994	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

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
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)