Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.12 kDa 
• Atom Count: 1103 
• Modelled Residue Count: 95 
• Deposited Residue Count: 95 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1B69

THE SOLUTION STRUCTURE OF TN916 INTEGRASE N-TERMINAL DOMAIN/DNA COMPLEX

• DOI: 10.2210/pdb1B69/pdb
• BMRB: 4165
• NDB: 1B69

• Classification: INTEGRASE/DNA
• Organism(s): synthetic construct, Enterococcus faecalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1999-01-21 Released: 1999-09-29 
• Deposition Author(s): Clubb, R.T., Wojciak, J.M., Connolly, K.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Literature

NMR structure of the Tn916 integrase-DNA complex.

Wojciak, J.M., Connolly, K.M., Clubb, R.T.

(1999) Nat Struct Biol 6: 366-373

• PubMed: 10201406 
• DOI: 10.1038/7603
• Primary Citation of Related Structures:  
  1B69, 1TN9


• PubMed Abstract: 
  

The integrase protein catalyzes the excision and integration of the Tn916 conjugative transposon, a promiscuous genetic element that spreads antibiotic resistance in pathogenic bacteria. The solution structure of the N-terminal domain of the Tn916 integrase protein bound to its DNA-binding site within the transposon arm has been determined. The structure reveals an interesting mode of DNA recognition, in which the face of a three-stranded antiparallel beta-sheet is positioned within the major groove. A comparison to the structure of the homing endonuclease I-Ppol-DNA complex suggests that the three-stranded sheet may represent a new DNA-binding motif whose residue composition and position within the major groove are varied to alter specificity. The structure also provides insights into the mechanism of conjugative transposition. The DNA in the complex is bent approximately 35 degrees and may, together with potential interactions between bound integrase proteins at directly repeated sites, significantly bend the arms of the transposon.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (INTEGRASE)	C [auth A]	69	Enterococcus faecalis	Mutation(s): 1  Gene Names: Int-Tn
UniProt
Find proteins for P22886 (Enterococcus faecalis) Explore P22886  Go to UniProtKB:  P22886

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*GP*TP*AP*GP*TP*AP*AP*AP*TP*TP*C)-3')	A [auth B]	13	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*AP*TP*TP*TP*AP*CP*TP*AP*CP*TP*C)-3')	B [auth C]	13	synthetic construct

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1B69	Kd: 151 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: LEAST RESTRAINT VIOLATION 
• OLDERADO: 1B69 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-21 
• Released Date: 1999-09-29 
Deposition Author(s): Clubb, R.T., Wojciak, J.M., Connolly, K.M.

Revision History  

• Version 1.0: 1999-09-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-14
  Changes: Database references, Derived calculations
• Version 2.0: 2019-10-16
  Changes: Atomic model, Data collection, Derived calculations, Source and taxonomy