5A6D | pdb_00005a6d

Proliferating Cell Nuclear Antigen, PCNA, from Thermococcus gammatolerans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.238 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.188 (Depositor) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Cloning, recombinant production and crystallographic structure of Proliferating Cell Nuclear Antigen from radioresistant archaeon Thermococcus gammatolerans.

Venancio-Landeros, A.A.Rudino-Pinera, E.Cardona-Felix, C.S.

(2016) Biochem Biophys Rep 8: 200-206

  • DOI: https://doi.org/10.1016/j.bbrep.2016.08.004
  • Primary Citation Related Structures: 
    5A6D

  • PubMed Abstract: 

    Thermococcus gammatolerans is a strictly anaerobic; hyperthermophilicarchaeon belongs to the order Thermococcales in the phylum Euryarchaeota . It was extracted from a hydrothermal vent from the Guaymas Basin (Gulf of California, Mexico). Different studies show that T. gammatolerans is one of the most radioresistant organisms known amongst the archaea . This makes it a unique model to study adaptations to the environment and to study DNA repair mechanisms in an organism able to tolerate harsh conditions. A key protein in these mechanisms is the Proliferation Cell Nuclear Antigen (PCNA). Its function is focused on their ability to slide along the DNA duplex and coordinating the activities of proteins mainly related to DNA edition and processing. Analysis of archaeal proteins have proven to be enormously fruitful because much of the information obtained from them can be extrapolated to eukaryotic systems, and PCNA is no exception. Here we report the cloning, recombinant expression and crystallographic structure of PCNA from T. gammatolerans (TgPCNA).


  • Organizational Affiliation
    • Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM),Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca 62210, Mexico.

Macromolecule Content 

  • Total Structure Weight: 56.31 kDa 
  • Atom Count: 3,898 
  • Modeled Residue Count: 492 
  • Deposited Residue Count: 498 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA POLYMERASE SLIDING CLAMP
A, B
249Thermococcus gammatolerans EJ3Mutation(s): 0 
UniProt
Find proteins for C5A5N6 (Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3))
Explore C5A5N6 
Go to UniProtKB:  C5A5N6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5A5N6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.238 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.188 (Depositor) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.669α = 90
b = 92.669β = 90
c = 63.632γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description