4DA2 | pdb_00004da2

The structure of Pyrococcus Furiosus SfsA in complex with Ca2+

• PDB DOI: https://doi.org/10.2210/pdb4DA2/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-12 Released: 2014-10-15 
• Deposition Author(s): Baker, P.J., Allen, F.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Literature

The structure of SfsA and its DNA complex; A DNA/RNA nuclease with a novel domain combination

Allen, F.L., Akerboom, J., Bliss, S.J., Blombach, F., Sedelnikova, S.E., van der Oost, J., Baker, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.62 kDa 
• Atom Count: 3,844 
• Modeled Residue Count: 462 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar fermentation stimulation protein homolog	A, B	231	Pyrococcus furiosus DSM 3638	Mutation(s): 1  Gene Names: PF1198, sfsA
UniProt
Find proteins for Q8U1K8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1K8  Go to UniProtKB:  Q8U1K8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.017	α = 90
b = 46.017	β = 90
c = 194.575	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Baker, P.J., Allen, F.L.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary