9PYO | pdb_00009pyo

Crystal structure of Fe/2-OG dependent dioxygenase MysH in complex with iron and 2-oxoglutarate

PDB DOI: https://doi.org/10.2210/pdb9PYO/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Nostoc linckia
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-08 Released: 2026-05-06
Deposition Author(s): Wanniarachchi, T.N., Bruner, S.D.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.208 (Depositor), 0.209 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of non-heme iron and 2-oxoglutarate dependent dioxygenase

Wanniarachchi, T.N., Bruner, S.D.

To be published.

Macromolecule Content

Total Structure Weight: 31.32 kDa
Atom Count: 2,260
Modeled Residue Count: 249
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe/2-OG dependent dioxygenase MysH	A	270	Nostoc linckia	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG (Subject of Investigation/LOI) Query on AKG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.208 (Depositor), 0.209 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.495	α = 90
b = 44.495	β = 90
c = 107.316	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Wanniarachchi, T.N.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2108383

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release

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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.