7M7K

Crystal structure of uridine bound to Geobacillus thermoglucosidasius pyrimidine nucleoside phosphorylase PyNP

• PDB DOI: https://doi.org/10.2210/pdb7M7K/pdb

• Classification: TRANSFERASE
• Organism(s): Parageobacillus thermoglucosidasius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-28 Released: 2021-08-25 
• Deposition Author(s): Pausch, P., Bange, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

Diversification of 4'-Methylated Nucleosides by Nucleoside Phosphorylases

Kaspar, F., Seeger, M., Westarp, S., Kollmann, C., Lehmann, A.P., Pausch, P., Kemper, S., Neubauer, P., Bange, G., Schallmey, A., Werz, D.B., Kurreck, A.

(2021) ACS Catal : 10830-10835

• DOI: https://doi.org/10.1021/acscatal.1c02589

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 47.4 kDa 
• Atom Count: 3,621 
• Modelled Residue Count: 432 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidine-nucleoside phosphorylase	A [auth B]	438	Parageobacillus thermoglucosidasius	Mutation(s): 0  Gene Names: DV714_16680 EC: 2.4.2.2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URI (Subject of Investigation/LOI)	E [auth B]	URIDINE C9 H12 N2 O6 DRTQHJPVMGBUCF-XVFCMESISA-N
SO4	B, C [auth B], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.262	α = 90
b = 84.262	β = 90
c = 121.694	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Pausch, P., Bange, G.

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description