3PZW

Soybean lipoxygenase-1 - re-refinement


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Determination of protein structures - a series of fortunate events.

Chruszcz, M.Wlodawer, A.Minor, W.

(2008) Biophys J 95: 1-9

  • DOI: https://doi.org/10.1529/biophysj.108.131789
  • Primary Citation of Related Structures:  
    3PZW

  • PubMed Abstract: 

    Determination of a macromolecular structure using x-ray diffraction is a multistep process that involves a plethora of techniques involving molecular biology, bioinformatics, and physical sciences. Counterintuitively, the success of any or all individual steps does not guarantee the success of the overall process. This review examines the difficulties presented by each step on the path from a gene to the final publication, together with certain lucky (or unlucky) circumstances that can affect the velocity along that path.


  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Seed lipoxygenase-1839Glycine maxMutation(s): 0 
Gene Names: LOX1.1LOX1
EC: 1.13.11.12
UniProt
Find proteins for P08170 (Glycine max)
Explore P08170 
Go to UniProtKB:  P08170
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08170
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.9α = 90
b = 94β = 90.1
c = 49.9γ = 90
Software Package:
Software NamePurpose
CHESS_A1data collection
HKL-3000phasing
REFMACrefinement
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Refinement description