5CHI

Crystal structure of PF2046 in complex with ssDNA

• PDB DOI: https://doi.org/10.2210/pdb5CHI/pdb
• NAKB: 5CHI

• Classification: HYDROLASE/DNA
• Organism(s): Pyrococcus furiosus DSM 3638, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-10 Released: 2016-08-10 
• Deposition Author(s): Kim, J.S., Hwang, K.Y., Lee, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.228 
• R-Value Work: 0.182 
• R-Value Observed: 0.186 

Literature

Structural basis of two-nucleotide removal of ssDNA by a cryptic RNase H fold 3'-5' exonuclease PF2046 from Pyrococcus furiosus

Kim, J.S., Sambalkhundev, G.D., Kim, S.H., Han, A., Ko, S.M., Hwang, K.Y., Lee, W.C.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.9 kDa 
• Atom Count: 5,755 
• Modelled Residue Count: 699 
• Deposited Residue Count: 702 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C	230	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF2046
UniProt
Find proteins for Q8TZE9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZE9  Go to UniProtKB:  Q8TZE9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*T)-3')	D, E, F	4	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	G [auth A], H [auth A], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.228 
• R-Value Work: 0.182 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.01	α = 90
b = 85.903	β = 118.44
c = 69.204	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Kim, J.S., Hwang, K.Y., Lee, W.C.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description