7D8J | pdb_00007d8j

S. aureus SsbB with 5-FU

PDB DOI: https://doi.org/10.2210/pdb7D8J/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus ED98
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-08 Released: 2020-12-23
Deposition Author(s): Lin, E.S., Huang, Y.H., Huang, C.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.194 (Depositor), 0.197 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the single-stranded DNA-binding protein SsbB in complex with the anticancer drug 5-fluorouracil: Extension of the 5-fluorouracil interactome to include the oligonucleotide/oligosaccharide-binding fold protein

Lin, E.S., Huang, C.Y.

(2020) Biochem Biophys Res Commun 534: 41-46

DOI: https://doi.org/10.1016/j.bbrc.2020.11.125

Macromolecule Content

Total Structure Weight: 26.9 kDa
Atom Count: 1,662
Modeled Residue Count: 210
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, B	118	Staphylococcus aureus subsp. aureus ED98	Mutation(s): 0
UniProt
Find proteins for A0A3F2YLU4 (Staphylococcus aureus (strain ED98)) Explore A0A3F2YLU4 Go to UniProtKB: A0A3F2YLU4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3F2YLU4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URF (Subject of Investigation/LOI) Query on URF Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	5-FLUOROURACIL C₄ H₃ F N₂ O₂ GHASVSINZRGABV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.257 (Depositor), 0.260 (DCC)
R-Value Work: 0.194 (Depositor), 0.197 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.366	α = 90
b = 116.366	β = 90
c = 78.538	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
HKL-2000	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-12-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-12-23
Type: Initial release
Version 1.1: 2023-11-29
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.