7EUT | pdb_00007eut

Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine

• PDB DOI: https://doi.org/10.2210/pdb7EUT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cercospora sojina
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-18 Released: 2022-05-25 
• Deposition Author(s): Hou, X.D., Liu, X.Z., Yuan, Z.B., Yin, D.J., Rao, Y.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed by Fe(II)/alpha-KG-Dependent Oxygenase CTB9

Liu, X.Z., Yuan, Z.B., Su, H., Hou, X.D., Deng, Z.W., Xu, H.B., Guo, B.D., Yin, D., Sheng, X., Rao, Y.J.

(2022) ACS Catal 12: 3689-3699

• DOI: https://doi.org/doi.org/10.1021/acscatal.1c04627

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.75 kDa 
• Atom Count: 5,082 
• Modeled Residue Count: 576 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate (2-OG)-dependent dioxygenase	A, B	333	Cercospora sojina	Mutation(s): 0  EC: 1
UniProt
Find proteins for A0A2G5I8W0 (Cercospora beticola) Explore A0A2G5I8W0  Go to UniProtKB:  A0A2G5I8W0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA	D [auth A], F [auth B]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	C [auth A], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.958	α = 90
b = 100.945	β = 93.72
c = 154.506	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data scaling
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Hou, X.D., Liu, X.Z., Yuan, Z.B., Yin, D.J., Rao, Y.J.

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Funding Organization	Location	Grant Number
Other private	China	2018YFA0901700
Other private	China	JUSRP12015
Other private	China	2020M671329
Other private	China	2020Z383

Revision History  

• Version 1.0: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description