Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.54 kDa 
• Atom Count: 1109 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

5NBJ

DLS Tetragonal - ReHEWL

• PDB DOI: 10.2210/pdb5NBJ/pdb

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


• Deposited: 2017-03-02 Released: 2017-05-10 
• Deposition Author(s): Brink, A., Helliwell, J.R.
• Funding Organization(s): National Research Foundation, SASOL University Collaboration Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.197 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

New leads for fragment-based design of rhenium/technetium radiopharmaceutical agents.

Brink, A., Helliwell, J.R.

(2017) IUCrJ 4: 283-290

• PubMed: 28512575 
• DOI: 10.1107/S2052252517003475
• Primary Citation of Related Structures:  
  5NBJ


• PubMed Abstract: 
  

Multiple possibilities for the coordination of fac -[Re(CO) ₃ (H ₂ O) ₃ ] ⁺ to a protein have been determined and include binding to Asp, Glu, Arg and His amino-acid residues as well as to the C-terminal carboxylate in the vicinity of Leu and Pro. The large number of rhenium metal complex binding sites that have been identified on specific residues thereby allow increased target identification for the design of future radiopharmaceuticals. The core experimental concept involved the use of state-of-art tuneable synchrotron radiation at the Diamond Light Source to optimize the rhenium anomalous dispersion signal to a large value ( f '' of 12.1 electrons) at its L _I absorption edge with a selected X-ray wavelength of 0.9763 Å. At the Cu  K α X-ray wavelength (1.5418 Å) the f '' for rhenium is 5.9 electrons. The expected peak-height increase owing to the optimization of the Re f '' was therefore 2.1. This X-ray wavelength tuning methodology thereby showed the lower occupancy rhenium binding sites as well as the occupancies of the higher occupancy rhenium binding sites.

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Organizational Affiliation: 

School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, England.

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RE	B [auth A], C [auth A], D [auth A], E [auth A], H [auth A], J [auth A], K [auth A], M [auth A], N [auth A], O [auth A]	RHENIUM Re WUAPFZMCVAUBPE-UHFFFAOYSA-N
CL	F [auth A], G [auth A], I [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.197 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data DOI: 10.5281/zenodo.345364 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.89	α = 90
b = 79.89	β = 90
c = 37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-03-02 
• Released Date: 2017-05-10 
Deposition Author(s): Brink, A., Helliwell, J.R.

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Funding Organization	Location	Grant Number
National Research Foundation	South Africa	UID 84266 & 99139
SASOL University Collaboration Initiative	South Africa	--

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Database references
• Version 1.2: 2018-08-08
  Changes: Data collection, Database references
• Version 1.3: 2019-09-18
  Changes: Data collection
• Version 1.4: 2019-11-20
  Changes: Derived calculations