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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6TK9

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B, C, D, E 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	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] 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		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.266 (Depositor), 0.266 (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

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Entry History

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Abramchik, Y.A.

Kostromina, M.A.

Revision History (Full details and data files)

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

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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.