1GEF

Crystal structure of the archaeal holliday junction resolvase HJC

• PDB DOI:  https://doi.org/10.2210/pdb1GEF/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2000-11-08 Released: 2001-03-21 
• Deposition Author(s): Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.224 

Literature

Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition.

Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y., Morikawa, K.

(2001) Structure 9: 197-204

• PubMed: 11286886 
• DOI: https://doi.org/10.1016/s0969-2126(01)00576-7
• Primary Citation of Related Structures:  
  1GEF


• PubMed Abstract: 
  

  Homologous recombination is a crucial mechanism in determining genetic diversity and repairing damaged chromosomes. Holliday junction is the universal DNA intermediate whose interaction with proteins is one of the major events in the recombinational process. Hjc is an archaeal endonuclease, which specifically resolves the junction DNA to produce two separate recombinant DNA duplexes. The atomic structure of Hjc should clarify the mechanisms of the specific recognition with Holliday junction and the catalytic reaction.

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Organizational Affiliation: 

Department of Structural Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 55.36 kDa 
• Atom Count: 3,951 
• Modelled Residue Count: 459 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HOLLIDAY JUNCTION RESOLVASE	A, B, C [auth D], D [auth E]	123	Pyrococcus furiosus	Mutation(s): 0  Gene Names: hjc EC: 3.1.21.10
UniProt
Find proteins for E7FHX4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore E7FHX4  Go to UniProtKB:  E7FHX4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.245	α = 90
b = 119.056	β = 90.66
c = 63.146	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-21 
Deposition Author(s): Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y., Morikawa, K.

Revision History  

• Version 1.0: 2001-03-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance