4WA8 | pdb_00004wa8

Methanopyrus Kandleri FEN-1 nuclease

• PDB DOI: https://doi.org/10.2210/pdb4WA8/pdb

• Classification: HYDROLASE
• Organism(s): Methanopyrus kandleri AV19
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-28 Released: 2014-11-12 
• Deposition Author(s): Shah, S., Dunten, P., Horton, N.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.231 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structure and specificity of FEN-1 from Methanopyrus kandleri.

Shah, S., Dunten, P., Stiteler, A., Park, C.K., Horton, N.C.

(2015) Proteins 83: 188-194

• PubMed: 25354467 
• DOI: https://doi.org/10.1002/prot.24704
• Primary Citation Related Structures: 
  4WA8


• PubMed Abstract: 
  

  DNA repair is fundamental to genome stability and is found in all three domains of life. However many archaeal species, such as Methanopyrus kandleri, contain only a subset of the eukaryotic nucleotide excision repair (NER) homologs, and those present often contain significant differences compared to their eukaryotic homologs. To clarify the role of the NER XPG-like protein Mk0566 from M. kandleri, its biochemical activity and three-dimensional structure were investigated. Both were found to be more similar to human FEN-1 than human XPG, suggesting a biological role in replication and long-patch base excision repair rather than in NER.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721.

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: 82.18 kDa 
• Atom Count: 4,842 
• Modeled Residue Count: 592 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flap endonuclease 1	A, B	355	Methanopyrus kandleri AV19	Mutation(s): 0  Gene Names: fen, MK0566 EC: 3.1
UniProt
Find proteins for Q8TXU4 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore Q8TXU4  Go to UniProtKB:  Q8TXU4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.231 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.331	α = 90
b = 86.193	β = 90
c = 147.617	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Shah, S., Dunten, P., Horton, N.C.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy