9HDL

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: in silico

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

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Friedrich, F., Genz, F., Einsle, O., Mueller, M., Fessner, N.D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release