1OSL

Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence

• PDB DOI: https://doi.org/10.2210/pdb1OSL/pdb
• NAKB: 1OSL
• BMRB: 5791

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-03-20 Released: 2004-05-04 
• Deposition Author(s): Kalodimos, C.G., Bonvin, A.M.J.J., Boelens, R., Kaptein, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 400 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.

Kalodimos, C.G., Biris, N., Bonvin, A.M., Levandoski, M.M., Guennuegues, M., Boelens, R., Kaptein, R.

(2004) Science 305: 386-389

• PubMed: 15256668 
• DOI: https://doi.org/10.1126/science.1097064
• Primary Citation of Related Structures:  
  1OSL


• PubMed Abstract: 
  

  Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient finding of the target site.

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Organizational Affiliation: 

Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.67 kDa 
• Atom Count: 1,685 
• Modelled Residue Count: 160 
• Deposited Residue Count: 160 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose operon repressor	C [auth A], D [auth B]	62	Escherichia coli	Mutation(s): 1  Gene Names: LACI
UniProt
Find proteins for P03023 (Escherichia coli (strain K12)) Explore P03023  Go to UniProtKB:  P03023

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*AP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*TP*CP*G)-3'	A [auth C], B [auth D]	18	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 400 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-04 
Deposition Author(s): Kalodimos, C.G., Bonvin, A.M.J.J., Boelens, R., Kaptein, R.

Revision History  

• Version 1.0: 2004-05-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Data collection, Database references, Derived calculations