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), 0.291 (DCC)
R-Value Work:
0.215 (Depositor), 0.219 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 92.85 kDa
Atom Count: 6,510
Modeled Residue Count: 866
Deposited Residue Count: 866
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39142
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.293 (Depositor), 0.291 (DCC)
R-Value Work: 0.215 (Depositor), 0.219 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-11-23

Deposition Author(s):

Gabdoulkhakov, A.G.

Mikhailov, A.M.

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

Revision History (Full details and data files)

Version 1.0: 2016-11-23
Type: Initial release
Version 1.1: 2024-01-10
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.