5YYU | pdb_00005yyu

Crystal structure of Staphylococcus aureus single-stranded DNA-binding protein SsbB

• PDB DOI: https://doi.org/10.2210/pdb5YYU/pdb

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


• Deposited: 2017-12-11 Released: 2018-08-15 
• Deposition Author(s): Huang, Y.H., Huang, C.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 
  0.299 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Characterization of single-stranded DNA-binding protein SsbB from Staphylococcus aureus: SsbB cannot stimulate PriA helicase.

Chen, K.L., Cheng, J.H., Lin, C.Y., Huang, Y.H., Huang, C.Y.

(2018) RSC Adv 8: 28367-28375

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.64 kDa 
• Atom Count: 3,143 
• Modeled Residue Count: 399 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, B, C, D	112	Staphylococcus aureus subsp. aureus ED98	Mutation(s): 0
UniProt
Find proteins for A0A3F2YLU4 (Staphylococcus aureus (strain ED98)) Explore A0A3F2YLU4  Go to UniProtKB:  A0A3F2YLU4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free:  0.299 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.993	α = 90
b = 84.739	β = 90
c = 84.862	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Huang, Y.H., Huang, C.Y.

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description