6TK9 | pdb_00006tk9

Purine-nucleoside phosphorylase from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb6TK9/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus
• Expression System: Thermus thermophilus
• Mutation(s): No 


• Deposited: 2019-11-28 Released: 2020-12-16 
• Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Kostromina, M.A., Tuzova, E.S., Esipov, R.S., Kuranova, I.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Purine-nucleoside phosphorylase from Thermus thermophilus

Timofeev, V.I., Abramchik, Y.A., Kostromina, M.A., Tuzova, E.S., Esipov, R.S., Kuranova, I.P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 180.16 kDa 
• Atom Count: 12,777 
• Modelled Residue Count: 1,626 
• Deposited Residue Count: 1,626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B, C, D, E, F	271	Thermus thermophilus	Mutation(s): 0  Gene Names: TthHC11_05990 EC: 2.4.2.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.85	α = 90
b = 120.95	β = 90
c = 215.47	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Kostromina, M.A., Tuzova, E.S., Esipov, R.S., Kuranova, I.P.

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description