3PZW

Soybean lipoxygenase-1 - re-refinement

• PDB DOI: https://doi.org/10.2210/pdb3PZW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Glycine max
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-14 Released: 2011-01-19 
• Deposition Author(s): Chruszcz, M., Minor, W.

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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

Literature

Determination of protein structures - a series of fortunate events.

Chruszcz, M., Wlodawer, A., Minor, W.

(2008) Biophys J 95: 1-9

• PubMed: 18441029 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.89 kDa 
• Atom Count: 7,762 
• Modelled Residue Count: 820 
• Deposited Residue Count: 839 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seed lipoxygenase-1	A	839	Glycine max	Mutation(s): 0  Gene Names: LOX1.1, LOX1 EC: 1.13.11.12
UniProt
Find proteins for P08170 (Glycine max) Explore P08170  Go to UniProtKB:  P08170

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

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 = 94.9	α = 90
b = 94	β = 90.1
c = 49.9	γ = 90

Software Package:

Software Name	Purpose
CHESS_A1	data collection
HKL-3000	phasing
REFMAC	refinement
Coot	model building
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Chruszcz, M., Minor, W.

Revision History  

• 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