5ODN | pdb_00005odn

Salinibacter ruber Single-Strand Binding protein

• PDB DOI: https://doi.org/10.2210/pdb5ODN/pdb
• NAKB: 5ODN

• Classification: DNA BINDING PROTEIN
• Organism(s): Salinibacter ruber DSM 13855, Salinibacter ruber
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-06 Released: 2018-08-01 
• Deposition Author(s): Pierechod, M., Rothweiler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Salinibacter ruber Single-Strand Binding protein

Pierechod, M., Rothweiler, U.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 183.98 kDa 
• Atom Count: 7,084 
• Modeled Residue Count: 854 
• Deposited Residue Count: 1,598 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, B, C, D, E, F, G, H	196	Salinibacter ruber DSM 13855	Mutation(s): 0  Gene Names: ssb, SRU_0523
UniProt
Find proteins for Q2S565 (Salinibacter ruber (strain DSM 13855 / M31)) Explore Q2S565  Go to UniProtKB:  Q2S565

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*T)-3')	I, J [auth M], K [auth J], L [auth K], M [auth N], O [auth Q]	4	Salinibacter ruber

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*T)-3')	N [auth P], P [auth L]	3	Salinibacter ruber

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.47	α = 90
b = 123.5	β = 90
c = 205.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Pierechod, M., Rothweiler, U.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references
• Version 1.2: 2021-02-03
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description