3QNG | pdb_00003qng

Crystal Structure Analysis of Lysozyme-bound fac-[Re(CO)3(L-serine)]

• PDB DOI: https://doi.org/10.2210/pdb3QNG/pdb

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


• Deposited: 2011-02-08 Released: 2012-01-18 
• Deposition Author(s): Zobi, F., Spingler, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.217 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.183 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1021/ic2023314
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. [e-mail]

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: 14.83 kDa 
• Atom Count: 1,120 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
REJ	B [auth A]	Tricarbonyl (L-serine) rhenium(I) C6 H6 N O6 Re QKENEJKDFPJRFD-AIDJSRAFSA-M
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.217 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.183 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.343	α = 90
b = 78.343	β = 90
c = 36.546	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Zobi, F., Spingler, B.

Revision History  

• 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: 2024-11-20
  Changes: Structure summary