1L1G | pdb_00001l1g

The Structure of Porcine Pancreatic Elastase Complexed with Xenon and Bromide, Cryoprotected with Glycerol

• PDB DOI: https://doi.org/10.2210/pdb1L1G/pdb

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


• Deposited: 2002-02-16 Released: 2002-08-28 
• Deposition Author(s): Panjikar, S., Tucker, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.176 (DCC) 

Starting Model: experimental

Literature

Xenon derivatization of halide-soaked protein crystals.

Panjikar, S., Tucker, P.A.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1413-1420

• PubMed: 12198297 
• DOI: https://doi.org/10.1107/S0907444902011010
• Primary Citation Related Structures: 
  1L0Z, 1L1G


• PubMed Abstract: 
  

  Crystals of porcine pancreatic elastase can be derived by soaking in high-molarity bromide solutions. These crystals, either in a glycerol-based cryoprotectant solution or in paraffin oil, can be subsequently pressurized under a xenon atmosphere to incorporate xenon. When paraffin oil is used, a larger number of bromide ions are observed on the protein surface. Intensity data collected to lower energy than the bromine absorption edge can be used to determine the xenon position and the resultant phase information can be used to determine the bromine substructure from data collected to higher energy than the bromine absorption edge. The method would appear to have general applicability where large substructures need to be determined.

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Organizational Affiliation: 
• EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.91 kDa 
• Atom Count: 2,101 
• Modeled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELASTASE 1	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XE	L [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.176 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.28	α = 90
b = 57.7	β = 90
c = 74.11	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
SHARP	phasing
SHELXL-97	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-28 
Deposition Author(s): Panjikar, S., Tucker, P.A.

Revision History  

• Version 1.0: 2002-08-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary