7EUS

Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) from Cercospora sp. JNU001

PDB DOI: https://doi.org/10.2210/pdb7EUS/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., Rao, Y.J.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.220
R-Value Work: 0.177
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 78.24 kDa
Atom Count: 4,986
Modelled Residue Count: 580
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate (2-OG)-dependent dioxygenase	A, B	333	Cercospora sojina	Mutation(s): 0
UniProt
Find proteins for A0A2G5I8W0 (Cercospora beticola) Explore A0A2G5I8W0 Go to UniProtKB: A0A2G5I8W0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2G5I8W0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.220
R-Value Work: 0.177
R-Value Observed: 0.181
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.427	α = 90
b = 147.916	β = 105.92
c = 54.163	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AutoSol	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-05-25
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.