1C10

CRYSTAL STRUCTURE OF HEW LYSOZYME UNDER PRESSURE OF XENON (8 BAR)

• PDB DOI: https://doi.org/10.2210/pdb1C10/pdb

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


• Deposited: 1999-07-16 Released: 1999-07-22 
• Deposition Author(s): Prange, T., Schiltz, M., Pernot, L., Colloc'h, N., Longhi, S., Bourguet, W., Fourme, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Exploring hydrophobic sites in proteins with xenon or krypton.

Prange, T., Schiltz, M., Pernot, L., Colloc'h, N., Longhi, S., Bourguet, W., Fourme, R.

(1998) Proteins 30: 61-73

• PubMed: 9443341 
• Primary Citation of Related Structures:  
  1C10, 1C1M, 1C3L, 1QTK


• PubMed Abstract: 
  

  X-ray diffraction is used to study the binding of xenon and krypton to a variety of crystallised proteins: porcine pancreatic elastase; subtilisin Carlsberg from Bacillus licheniformis; cutinase from Fusarium solani; collagenase from Hypoderma lineatum; hen egg lysozyme, the lipoamide dehydrogenase domain from the outer membrane protein P64k from Neisseria meningitidis; urate-oxidase from Aspergillus flavus, mosquitocidal delta-endotoxin CytB from Bacillus thuringiensis and the ligand-binding domain of the human nuclear retinoid-X receptor RXR-alpha. Under gas pressures ranging from 8 to 20 bar, xenon is able to bind to discrete sites in hydrophobic cavities, ligand and substrate binding pockets, and into the pore of channel-like structures. These xenon complexes can be used to map hydrophobic sites in proteins, or as heavy-atom derivatives in the isomorphous replacement method of structure determination.

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Organizational Affiliation: 

LURE, Université Paris-Sud, Orsay, France. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.96 kDa 
• Atom Count: 1,080 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XE	I [auth A], J [auth A], K [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Observed: 0.170 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.53	α = 90
b = 78.53	β = 90
c = 37.74	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CCP4	model building
SHELXL-97	refinement
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-22 
Deposition Author(s): Prange, T., Schiltz, M., Pernot, L., Colloc'h, N., Longhi, S., Bourguet, W., Fourme, R.

Revision History  

• Version 1.0: 1999-07-22
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary