1L1G

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Xenon derivatization of halide-soaked protein crystals.

Panjikar, S., Tucker, P.A.

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

  • DOI: https://doi.org/10.1107/S0907444902011010
  • Primary Citation of 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.

    • Organizational Affiliation: 

    EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, Germany.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ELASTASE 1240Sus scrofaMutation(s): 0 
EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa)
Explore P00772 
Go to UniProtKB:  P00772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00772
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XE
Query on XE
Download Ideal Coordinates CCD File 
L [auth A]XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
SO4
Query on SO4
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B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL
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M [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR
Query on BR
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D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
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
Query on NA
Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.28α = 90
b = 57.7β = 90
c = 74.11γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
SHARPphasing
SHELXL-97refinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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