5EEO | pdb_00005eeo

soybean lipoxygenase(L1)-T756R

• PDB DOI: https://doi.org/10.2210/pdb5EEO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Glycine max
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-10-23 Released: 2015-11-25 
• Deposition Author(s): Mikami, B., Nagaya, T., Hioki, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

The structural basis for specificity in lipoxygenase catalysis

Mikami, B., Nagaya, T., Hioki, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.59 kDa 
• Atom Count: 6,877 
• Modeled Residue Count: 806 
• Deposited Residue Count: 839 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seed linoleate 13S-lipoxygenase-1	A	839	Glycine max	Mutation(s): 1  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.708	α = 90
b = 62.361	β = 103.25
c = 92.351	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Mikami, B., Nagaya, T., Hioki, Y.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description