1C1M

PORCINE ELASTASE UNDER XENON PRESSURE (8 BAR)

• PDB DOI: https://doi.org/10.2210/pdb1C1M/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 1999-07-22 Released: 1999-07-28 
• 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: 2.20 Å
• R-Value Free: 0.201 
• R-Value Observed: 0.162 

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: 26.2 kDa 
• Atom Count: 1,957 
• Modelled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PORCINE ELASTASE)	A	240	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XE	D [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.201 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.19	α = 90
b = 58.22	β = 90
c = 75.77	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-28 
Deposition Author(s): Prange, T., Schiltz, M., Pernot, L., Colloc'h, N., Longhi, S., Bourguet, W., Fourme, R.

Revision History  

• Version 1.0: 1999-07-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary