7DEP

S. aureus SsbB with 5-FU

PDB DOI: https://doi.org/10.2210/pdb7DEP/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus ED98
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-04 Released: 2020-12-23
Deposition Author(s): Lin, E.S., Huang, Y.H., Huang, C.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.271
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

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: 25.58 kDa
Atom Count: 1,600
Modelled Residue Count: 201
Deposited Residue Count: 224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, B	112	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 Query on URF 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]	C [auth A], D [auth B]	5-FLUOROURACIL C₄ H₃ F N₂ O₂ GHASVSINZRGABV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.271
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.962	α = 90
b = 116.962	β = 90
c = 77.713	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

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

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 R01GM133198.