5ODP | pdb_00005odp

Salinibacter ruber Single-Strand Binding protein D17K D71K mutant

• PDB DOI: https://doi.org/10.2210/pdb5ODP/pdb
• NAKB: 5ODP

• Classification: DNA BINDING PROTEIN
• Organism(s): Salinibacter ruber DSM 13855, Salinibacter ruber
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.54 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Salinibacter ruber Single-Strand Binding protein D17K D71K mutant

Pierechod, M., Rothweiler, U.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.84 kDa 
• Atom Count: 1,862 
• Modeled Residue Count: 220 
• Deposited Residue Count: 442 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, B [auth G]	196	Salinibacter ruber DSM 13855	Mutation(s): 2  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(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')	C [auth L], D [auth M], E [auth N], F [auth O], G [auth P]	10	Salinibacter ruber

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.587	α = 90
b = 102.587	β = 90
c = 61.502	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