1T3P | pdb_00001t3p

Half-sandwich arene ruthenium(II)-enzyme complex

PDB DOI: https://doi.org/10.2210/pdb1T3P/pdb

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

Deposited: 2004-04-27 Released: 2005-07-26
Deposition Author(s): McNae, I.W., Fishburne, K., Habtemariam, A., Hunter, T.M., Melchart, M., Wang, F., Walkinshaw, M.D., Sadler, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.217 (Depositor), 0.228 (DCC)
R-Value Work:
0.182 (Depositor), 0.193 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Half-sandwich arene ruthenium(II)-enzyme complex

McNae, I.W., Fishburne, K., Habtemariam, A., Hunter, T.M., Melchart, M., Wang, F., Walkinshaw, M.D., Sadler, P.J.

(2004) Chem Commun (Camb) 16: 1786-1787

PubMed: 15306883 Search on PubMed
DOI: https://doi.org/10.1039/b408141b
Primary Citation Related Structures:
1T3P

PubMed Abstract:
The 1.6 [Angstrom] X-ray crystal structure of [(eta(6)-p-cymene)Ru(lysozyme)Cl(2)], the first of a half-sandwich complex of a protein, shows selective ruthenation of Nepsilon of the imidazole ring of His15.

Organizational Affiliation

Institute of Cell and Molecular Biology, Michael Swann Building, University of Edinburgh, Mayfield Road, Edinburgh, UK.

Macromolecule Content

Total Structure Weight: 14.79 kDa
Atom Count: 1,209
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RU7 Query on RU7 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PARA-CYMENE RUTHENIUM CHLORIDE C₁₀ H₁₄ Cl₂ Ru UCXDWSTYBSBFFB-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.217 (Depositor), 0.228 (DCC)
R-Value Work: 0.182 (Depositor), 0.193 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.142	α = 90
b = 80.142	β = 90
c = 37.064	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-07-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-07-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary