5EP8 | pdb_00005ep8

X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis with Sulfate Ion

• PDB DOI: https://doi.org/10.2210/pdb5EP8/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-11 Released: 2016-11-23 
• Deposition Author(s): Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.
• Funding Organization(s): RFBR

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis with Sulfate Ion

Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

To be published.

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: 92.85 kDa 
• Atom Count: 6,510 
• Modelled Residue Count: 866 
• Deposited Residue Count: 866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidine-nucleoside phosphorylase	A, B	433	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: pdp, BSU39400 EC: 2.4.2.2
UniProt
Find proteins for P39142 (Bacillus subtilis (strain 168)) Explore P39142  Go to UniProtKB:  P39142

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.463	α = 90
b = 91.35	β = 90
c = 109.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

---

Funding Organization	Location	Grant Number
RFBR	Russian Federation	14-04-00952

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description