3OPX | pdb_00003opx

Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate

PDB DOI: https://doi.org/10.2210/pdb3OPX/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-09-02 Released: 2011-03-02
Deposition Author(s): Teng, M.K., Niu, L.W., Shi, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.251 (Depositor), 0.248 (DCC)
R-Value Work:
0.212 (Depositor), 0.212 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate

Shi, N., Teng, M.K., Niu, L.W.

To be published.

Macromolecule Content

Total Structure Weight: 30.54 kDa
Atom Count: 2,175
Modeled Residue Count: 247
Deposited Residue Count: 263
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SSM1	A	263	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: SSM1, SDT1, YGL224C
UniProt
Find proteins for P53078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53078 Go to UniProtKB: P53078
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53078
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.251 (Depositor), 0.248 (DCC)
R-Value Work: 0.212 (Depositor), 0.212 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.198	α = 90
b = 78.037	β = 90
c = 82.789	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.