6D0O

rdpA dioxygenase holoenzyme

• PDB DOI: https://doi.org/10.2210/pdb6D0O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphingobium herbicidovorans NBRC 16415
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-10 Released: 2018-08-15 
• Deposition Author(s): Rydel, T.J., Sturman, E.J., Zheng, M., Evdokimov, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops.

Larue, C.T., Goley, M., Shi, L., Evdokimov, A.G., Sparks, O.C., Ellis, C., Wollacott, A.M., Rydel, T.J., Halls, C.E., Van Scoyoc, B., Fu, X., Nageotte, J.R., Adio, A.M., Zheng, M., Sturman, E.J., Garvey, G.S., Varagona, M.J.

(2019) Pest Manag Sci 75: 2086-2094

• PubMed: 30828945 
• DOI: https://doi.org/10.1002/ps.5393
• Primary Citation of Related Structures:  
  6D0O, 6D1O, 6D3H, 6D3I, 6D3J, 6D3M


• PubMed Abstract: 
  

  Effective management of weedy species in agricultural fields is essential for maintaining favorable growing conditions and crop yields. The introduction of genetically modified crops containing herbicide tolerance traits has been a successful additional tool available to farmers to better control weeds. However, weed resistance challenges present a need for additional herbicide tolerance trait options.

---

Organizational Affiliation: 

Bayer Crop Science, Plant Biotechnology, Chesterfield, MO, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 136.73 kDa 
• Atom Count: 9,524 
• Modelled Residue Count: 1,117 
• Deposited Residue Count: 1,204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase	A, B, C, D	301	Sphingobium herbicidovorans NBRC 16415	Mutation(s): 0  Gene Names: rdpA EC: 1.14.11.44
UniProt
Find proteins for Q8KSC8 (Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 / MH)) Explore Q8KSC8  Go to UniProtKB:  Q8KSC8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	F [auth A], H [auth B], J [auth C], L [auth D]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
CO	E [auth A], G [auth B], I [auth C], K [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.014	α = 90
b = 153.014	β = 90
c = 156.845	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Rydel, T.J., Sturman, E.J., Zheng, M., Evdokimov, A.

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Database references
• Version 1.3: 2024-03-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description