9HDL | pdb_00009hdl

Crystal structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) from Neurospora crassa

PDB DOI: https://doi.org/10.2210/pdb9HDL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Neurospora crassa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-12 Released: 2025-02-26
Deposition Author(s): Friedrich, F., Genz, F., Einsle, O., Mueller, M., Fessner, N.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

Identification and Characterization of Pyrimidine Nucleoside 2'-Hydroxylase

Genz, F., Friedrich, F., Lonarz, C., Einsle, O., Jung, M., Muller, M., Fessner, N.D.

(2025) ACS Catal

DOI: https://doi.org/10.1021/acscatal.4c07764

Macromolecule Content

Total Structure Weight: 42.56 kDa
Atom Count: 2,845
Modeled Residue Count: 344
Deposited Residue Count: 390
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clavaminate synthase-like protein	A	390	Neurospora crassa	Mutation(s): 0 Gene Names: NCU02560
UniProt
Find proteins for Q7SHQ5 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q7SHQ5 Go to UniProtKB: Q7SHQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SHQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE 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]	FE (III) ION Fe VTLYFUHAOXGGBS-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: 1.60 Å
R-Value Free: 0.213 (Depositor), 0.213 (DCC)
R-Value Work: 0.181 (Depositor), 0.181 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.105	α = 90
b = 61.744	β = 90
c = 84.325	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
autoPROC	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-02-26
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.