9CI4 | pdb_00009ci4

Crystal structure of Fe/2-OG dependent dioxygenase MysH (Apo form)

PDB DOI: https://doi.org/10.2210/pdb9CI4/pdb

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

Deposited: 2024-07-02 Released: 2026-03-18
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: 1.70 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of non-heme iron and alpha-ketoglutarate dependent dioxygenase MysH

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

To be published.

Macromolecule Content

Total Structure Weight: 31.24 kDa
Atom Count: 2,248
Modeled Residue Count: 248
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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 Gene Names: VF08_32425
UniProt
Find proteins for A0A9Q5Z5X5 (Nostoc linckia z8) Explore A0A9Q5Z5X5 Go to UniProtKB: A0A9Q5Z5X5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A9Q5Z5X5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.204 (Depositor), 0.204 (DCC)
R-Value Work: 0.175 (Depositor), 0.176 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.419	α = 90
b = 44.419	β = 90
c = 107.754	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-18

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: 2026-03-18
Type: Initial release

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.