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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.254 (Depositor), 0.255 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5EEO

This is version 1.2 of the entry. See complete history.

Literature

The structural basis for specificity in lipoxygenase catalysis

Mikami, B., Nagaya, T., Hioki, Y.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08170
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.254 (Depositor), 0.255 (DCC)
R-Value Work: 0.186 (Depositor), 0.187 (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

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Entry History

Deposition Data

Released Date: 2015-11-25

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.