9HMO | pdb_00009hmo

X-ray structure of the C-terminal domain (residues 366-485) of S. pombe threonylcarbamoyladenosine dehydratase

PDB DOI: https://doi.org/10.2210/pdb9HMO/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Schizosaccharomyces pombe
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-12-09 Released: 2025-12-24
Deposition Author(s): Hirschmann, J., Huber, E.M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.212 (Depositor), 0.220 (DCC)
R-Value Work:
0.173 (Depositor), 0.187 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and biochemical characterization of yeast Tcd enzymes installing the epigenetic modification ct6A in tRNA

Hirschmann, J., Sonntag, R., Heiss, M., Wegrzyn, E., Heinemeyer, W., Carell, T., Huber, E.M.

To be published.

Macromolecule Content

Total Structure Weight: 14.28 kDa
Atom Count: 1,065
Modeled Residue Count: 120
Deposited Residue Count: 121
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA threonylcarbamoyladenosine dehydratase	A	121	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: SPAC1A6.10, SPAC30D11.05c EC: 6.1
UniProt
Find proteins for O13861 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O13861 Go to UniProtKB: O13861
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O13861
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.212 (Depositor), 0.220 (DCC)
R-Value Work: 0.173 (Depositor), 0.187 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.45	α = 90
b = 55.49	β = 90
c = 69.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Arcimboldo	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	325871075

Revision History (Full details and data files)

Version 1.0: 2025-12-24
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.