1UO6 | pdb_00001uo6

PORCINE PANCREATIC ELASTASE/Xe-COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.208 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.178 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1UO6

This is version 1.4 of the entry. See complete history

Literature

On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part II. Data-Collection Wavelength and Scaling Models

Mueller-Dieckmann, C.Polentarutti, M.Djinovic-Carugo, K.Panjikar, S.Tucker, P.A.Weiss, M.S.

(2004) Acta Crystallogr D Biol Crystallogr 60: 28

  • DOI: https://doi.org/10.1107/s0907444903020833
  • Primary Citation Related Structures: 
    1UO6

  • PubMed Abstract: 

    Complete and highly redundant data sets were collected at nine different wavelengths between 0.80 and 2.65 A on a xenon derivative of porcine pancreatic elastase in both air and helium atmospheres. The magnitude of the anomalous signal, as assessed by the xenon-peak height in the anomalous difference Patterson synthesis, is affected by the wavelength of data collection as well as by the scaling model used. For data collected at wavelengths longer than 1.7 A, the use of a three-dimensional scaling protocol is essential in order to obtain the highest possible anomalous signal. Based on the scaling protocols currently available, the optimal wavelength range for data collection appears to be between 2.1 and 2.4 A. Beyond that, any further increase in signal will be compensated for or even superseded by a concomitant increase in noise, which cannot be fully corrected for. Data collection in a helium atmosphere yields higher I/sigma(I) values, but not significantly better anomalous differences, than data collection in air.


  • Organizational Affiliation
    • EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 26.4 kDa 
  • Atom Count: 2,086 
  • Modeled Residue Count: 240 
  • Deposited Residue Count: 240 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
G [auth A]XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.208 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.178 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.17α = 90
b = 58.06β = 90
c = 74.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary