3QE8

Crystal Structure Analysis of Lysozyme-bound fac-[Re(CO)3(H2O)(Im)]+

PDB DOI: https://doi.org/10.2210/pdb3QE8/pdb

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

Deposited: 2011-01-20 Released: 2012-01-18
Deposition Author(s): Zobi, F., Spingler, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.219
R-Value Observed: 0.197

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Post-protein-binding reactivity and modifications of the fac-[Re(CO)3]+ core

Zobi, F., Spingler, B.

(2012) Inorg Chem 51: 1210-1212

PubMed: 22229733 Search on PubMed
DOI: https://doi.org/10.1021/ic2023314
Primary Citation of Related Structures:
3QE8, 3QNG

PubMed Abstract:
The reactivity of the [Re(CO)(3)(H(2)O)(2)](+) complex coordinated to the His15 residue of HEW lysozyme is described. In the fully metalated protein (Lys-1), the Re ion retains its reactivity only toward selected ligands, while others induce a ligand-mediated demetalation of the enzyme. It is further shown that some of the complexes that may be "engineered" on the lysozyme do not react with the free protein even if present in solution in excess. The formation of stable metal adducts starting from Lys-1 was confirmed by X-ray crystallography.

Organizational Affiliation

Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. [email protected]

Macromolecule Content

Total Structure Weight: 29.61 kDa
Atom Count: 2,211
Modelled Residue Count: 258
Deposited Residue Count: 258
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, B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
REI Query on REI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	Tricarbonyl (aqua) (imidazole) rhenium(I) C₆ H₆ N₂ O₄ Re KPOHHEXTCRHHSE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.219
R-Value Observed: 0.197
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.896	α = 90
b = 77.996	β = 90
c = 80.081	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-18

Deposition Author(s):

Zobi, F.

Spingler, B.

Revision History (Full details and data files)

Version 1.0: 2012-01-18
Type: Initial release
Version 1.1: 2012-03-21
Changes: Database references
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary