1RRL

Soybean Lipoxygenase (LOX-3) at 93K at 2.0 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution.

Skrzypczak-Jankun, E., BORBULEVYCH, O.Y., ZAVODSZKY, M.I., BARANSKI, M.R., PADMANABHAN, K., PETRICEK, V., JANKUN, J.

(2006) Acta Crystallogr D Biol Crystallogr 62: 766-775

  • DOI: 10.1107/S0907444906016982
  • Primary Citation of Related Structures:  
    1RRH, 1RRL

  • PubMed Abstract: 

    • Flash-freezing is a technique that is commonly used nowadays to collect diffraction data for X-ray structural analysis. It can affect both the crystal and molecular structure and the molecule's surface, as well as the internal cavities. X-ray structural data often serve as a template for the protein receptor in docking calculations ...

    Flash-freezing is a technique that is commonly used nowadays to collect diffraction data for X-ray structural analysis. It can affect both the crystal and molecular structure and the molecule's surface, as well as the internal cavities. X-ray structural data often serve as a template for the protein receptor in docking calculations. Thus, the size and shape of the binding site determines which small molecules could be found as potential ligands in silico, especially during high-throughput rigid docking. Data were analyzed for wild soybean lipoxygenase-3 (MW 97 kDa) at 293 and 93 K and compared with the results from studies of its molecular complexes with known inhibitors, structures published by others for a derivative of the same enzyme (98 K) or a topologically close isozyme lipoxygenase-1 (at ambient temperature and 100 K). Analysis of these data allows the following conclusions. (i) Very small changes in the relative orientation of the molecules in the crystal can cause major changes in the crystal reciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing even when the unit-cell and the protein molecular volume show changes of only 1-2%. (iii) Using a receptor structure determined based on cryogenic data as a target for computational screening requires flexible docking to enable the expansion of the binding-site cavity and sampling of the alternative conformations of the crucial residues.

    Related Citations: 
    • Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme
      Skrzypczak-Jankun, E., Amzel, L.M., Kroa, B., Funk, M.O.
      (1997) Proteins 29: 15
    • Flash-freezing causes a stress induced modulation in a crystal structure of soybean lipoxygenase L3
      Skrzypczak-Jankun, E., Bianchet, M., Amzel, L.M., Funk, M.O.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 959
    Organizational Affiliation: 

    Urology Research Center, Medical University of Ohio, Toledo, OH 43614, USA. eskrzypczak@meduohio.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Seed lipoxygenase-3A, B857Glycine maxMutation(s): 0 
Gene Names: LOX1.3, LOX3
EC: 1.13.11.12 (PDB Primary Data), 1.13.11.58 (UniProt)
UniProt
Find proteins for P09186 (Glycine max)
Explore P09186 
Go to UniProtKB:  P09186
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09186
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.4α = 90
b = 133.5β = 97.3
c = 60.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
bioteXdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2012-02-08
    Changes: Derived calculations
  • Version 1.4: 2017-10-11
    Changes: Refinement description