2ZJA

Archaeal DNA helicase Hjm complexed with AMPPCP in form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm

Oyama, T.Oka, H.Mayanagi, K.Shirai, T.Matoba, K.Fujikane, R.Ishino, Y.Morikawa, K.

(2009) BMC Struct Biol 9: 2-2

  • DOI: https://doi.org/10.1186/1472-6807-9-2
  • Primary Citation of Related Structures:  
    2ZJ2, 2ZJ5, 2ZJ8, 2ZJA

  • PubMed Abstract: 

    Pyrococcus furiosus Hjm (PfuHjm) is a structure-specific DNA helicase that was originally identified by in vitro screening for Holliday junction migration activity. It belongs to helicase superfamily 2, and shares homology with the human DNA polymerase Theta (PolTheta), HEL308, and Drosophila Mus308 proteins, which are involved in DNA repair. Previous biochemical and genetic analyses revealed that PfuHjm preferentially binds to fork-related Y-structured DNAs and unwinds their double-stranded regions, suggesting that this helicase is a functional counterpart of the bacterial RecQ helicase, which is essential for genome maintenance. Elucidation of the DNA unwinding and translocation mechanisms by PfuHjm will require its three-dimensional structure at atomic resolution.


  • Organizational Affiliation

    The Takara Bio Endowed Division, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology (OLABB), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ski2-type helicase720Pyrococcus furiosusMutation(s): 0 
EC: 3.6.1
UniProt
Find proteins for O73946 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore O73946 
Go to UniProtKB:  O73946
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO73946
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.145α = 90
b = 81.627β = 112.83
c = 86.635γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description