1LZ8

LYSOZYME PHASED ON ANOMALOUS SIGNAL OF SULFURS AND CHLORINES

• PDB DOI: https://doi.org/10.2210/pdb1LZ8/pdb

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


• Deposited: 1999-03-14 Released: 1999-05-26 
• Deposition Author(s): Dauter, Z., Dauter, M., De La Fortelle, E., Bricogne, G., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.310 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

Can anomalous signal of sulfur become a tool for solving protein crystal structures?

Dauter, Z., Dauter, M., de La Fortelle, E., Bricogne, G., Sheldrick, G.M.

(1999) J Mol Biol 289: 83-92

• PubMed: 10339407 
• DOI: https://doi.org/10.1006/jmbi.1999.2743
• Primary Citation of Related Structures:  
  1LZ8


• PubMed Abstract: 
  

  A general method for solving the phase problem from native crystals of macromolecules has long eluded structural biology. For well diffracting crystals this goal can now be achieved, as is shown here, thanks to modern data collection techniques and new statistical phasing algorithms. Using solely a native crystal of tetragonal hen egg-white lysozyme, a protein of 14 kDa molecular mass, it was possible to detect the positions of the ten sulfur and seven chlorine atoms from their anomalous signal, and proceed from there to obtain an electron-density map of very high quality.

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Organizational Affiliation: 

National Cancer Institute, Frederick and Brookhaven National Laboratory, Building 725A-X9, Upton, NY, 11973, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.64 kDa 
• Atom Count: 1,234 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (LYSOZYME)	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.310 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.81	α = 90
b = 78.81	β = 90
c = 36.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-26 
Deposition Author(s): Dauter, Z., Dauter, M., De La Fortelle, E., Bricogne, G., Sheldrick, G.M.

Revision History  

• Version 1.0: 1999-05-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary