3JU0 | pdb_00003ju0

Structure of the arm-type binding domain of HAI7 integrase

• PDB DOI: https://doi.org/10.2210/pdb3JU0/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Pectobacterium atrosepticum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-14 Released: 2009-10-06 
• Deposition Author(s): Szwagierczak, A., Antonenka, U., Popowicz, G.M., Sitar, T., Holak, T.A., Rakin, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Structures of the arm-type binding domains of HPI and HAI7 integrases

Szwagierczak, A., Antonenka, U., Popowicz, G.M., Sitar, T., Holak, T.A., Rakin, A.

(2009) J Biological Chem 284: 31664-31671

• PubMed: 19737930 
• DOI: https://doi.org/10.1074/jbc.M109.059261
• Primary Citation Related Structures: 
  3JTZ, 3JU0


• PubMed Abstract: 
  

  The structures of the N-terminal domains of two integrases of closely related but not identical asn tDNA-associated genomic islands, Yersinia HPI (high pathogenicity island; encoding siderophore yersiniabactin biosynthesis and transport) and an Erwinia carotovora genomic island with yet unknown function, HAI7, have been resolved. Both integrases utilize a novel four-stranded beta-sheet DNA-binding motif, in contrast to the known proteins that bind their DNA targets by means of three-stranded beta-sheets. Moreover, the beta-sheets in Int(HPI) and Int(HAI7) are longer than those in other integrases, and the structured helical N terminus is positioned perpendicularly to the large C-terminal helix. These differences strongly support the proposal that the integrases of the genomic islands make up a distinct evolutionary branch of the site-specific recombinases that utilize a unique DNA-binding mechanism.

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Organizational Affiliation: 
• Max Planck Institute for Biochemistry, D-82152 Martinsried, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 12.53 kDa 
• Atom Count: 866 
• Modeled Residue Count: 95 
• Deposited Residue Count: 108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage integrase	A	108	Pectobacterium atrosepticum	Mutation(s): 0  Gene Names: intB, ECA1679
UniProt
Find proteins for Q6D6K1 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D6K1  Go to UniProtKB:  Q6D6K1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.53	α = 90
b = 52.53	β = 90
c = 79.47	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Szwagierczak, A., Antonenka, U., Popowicz, G.M., Sitar, T., Holak, T.A., Rakin, A.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-01-16
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Refinement description