9C9N | pdb_00009c9n

Crystal structure of Fe/2-OG dependent dioxygenase MysH in complex with nickel and succinate

• PDB DOI: https://doi.org/10.2210/pdb9C9N/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Nostoc linckia NIES-25
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-14 Released: 2025-10-08 
• Deposition Author(s): Wanniarachchi, T.N., Bruner, S.D.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of non-heme iron and alpha-ketoglutarate dependent dioxygenase MysH (To be published)

Wanniarachchi, T.N., Bruner, S.D.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 31.35 kDa 
• Atom Count: 2,363 
• Modeled Residue Count: 262 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe/2-OG dependent dioxygenase MysH	A	270	Nostoc linckia NIES-25	Mutation(s): 0
UniProt
Find proteins for A0A9Q5Z5X5 (Nostoc linckia z8) Explore A0A9Q5Z5X5  Go to UniProtKB:  A0A9Q5Z5X5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN (Subject of Investigation/LOI)	B [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI (Subject of Investigation/LOI)	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.291	α = 90
b = 44.291	β = 90
c = 107.349	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Wanniarachchi, T.N., Bruner, S.D.

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

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release