8S7B | pdb_00008s7b

Fe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase His1 in complex with 2-oxoglutarate

• PDB DOI: https://doi.org/10.2210/pdb8S7B/pdb

• Classification: OXYGEN BINDING
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-29 Released: 2025-03-12 
• Deposition Author(s): Dhingra, S., Alshref, F., Farcas, I.M., Brewitz, L., Allen, M.D., Schofield, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: in silico

Literature

Fe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase His1 in complex with 2-oxoglutarate

Dhingra, S., Alshref, F., Farcas, I.M., Brewitz, L., Allen, M.D., Schofield, C.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.22 kDa 
• Atom Count: 3,128 
• Modeled Residue Count: 350 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe(II)/2-oxoglutarate-dependent oxygenase	A	356	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: HIS1, LOC_Os02g17940, Os02g0280700, OSNPB_020280700
UniProt
Find proteins for Q6ES21 (Oryza sativa subsp. japonica) Explore Q6ES21  Go to UniProtKB:  Q6ES21

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE8 (Subject of Investigation/LOI)	D [auth A]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.332	α = 90
b = 67.432	β = 92.09
c = 83.176	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Dhingra, S., Alshref, F., Farcas, I.M., Brewitz, L., Allen, M.D., Schofield, C.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V001892/1

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release