7EUS | pdb_00007eus

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 (Depositor), 0.224 (DCC)
R-Value Work:
0.177 (Depositor), 0.186 (DCC)
R-Value Observed:
0.181 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 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
Modeled Residue Count: 580
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	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 (Depositor), 0.224 (DCC)
R-Value Work: 0.177 (Depositor), 0.186 (DCC)
R-Value Observed: 0.181 (Depositor)

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

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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
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary

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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.