Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 9.53 kDa 
• Atom Count: 706 
• Modelled Residue Count: 73 
• Deposited Residue Count: 83 
• Unique protein chains: 1

3ZHI

N-terminal domain of the CI repressor from bacteriophage TP901-1

• PDB DOI: 10.2210/pdb3ZHI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Lactococcus phage TP901-1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-12-21 Released: 2013-12-25 
• Deposition Author(s): Frandsen, K.H., Rasmussen, K.K., Poulsen, J.N., Lo Leggio, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.183 
• R-Value Work: 0.135 
• R-Value Observed: 0.137 

Literature

Binding of the N-Terminal Domain of the Lactococcal Bacteriophage Tp901-1 Ci Repressor to its Target DNA: A Crystallography, Small Angle Scattering, and Nuclear Magnetic Resonance Study.

Frandsen, K.H., Rasmussen, K.K., Jensen, M.R., Hammer, K., Pedersen, M., Poulsen, J.N., Arleth, L., Lo Leggio, L.

(2013) Biochemistry 52: 6892

• PubMed: 24047404 
• DOI: 10.1021/bi400439y
• Primary Citation of Related Structures:  
  3ZHI, 3ZHM


• PubMed Abstract: 
  

In most temperate bacteriophages, regulation of the choice of lysogenic or lytic life cycle is controlled by a CI repressor protein. Inhibition of transcription is dependent on a helix-turn-helix motif, often located in the N-terminal domain (NTD), which binds to specific DNA sequences (operator sites). Here the crystal structure of the NTD of the CI repressor from phage TP901-1 has been determined at 1.6 Å resolution, and at 2.6 Å resolution in complex with a 9 bp double-stranded DNA fragment that constitutes a half-site of the OL operator. This N-terminal construct, comprising residues 2-74 of the CI repressor, is monomeric in solution as shown by nuclear magnetic resonance (NMR), small angle X-ray scattering, and gel filtration and is monomeric in the crystal structures. The binding interface between the NTD and the half-site in the crystal is very similar to the interface that can be mapped by NMR in solution with a full palindromic site. The interactions seen in the complexes (in the crystal and in solution) explain the observed affinity for the OR site that is lower than that for the OL site and the specificity for the recognized DNA sequence in comparison to that for other repressors. Compared with many well-studied phage repressor systems, the NTD from TP901-1 CI has a longer extended scaffolding helix that, interestingly, is strongly conserved in putative repressors of Gram-positive pathogens. On the basis of sequence comparisons, we suggest that these bacteria also possess repressor/antirepressor systems similar to that found in phage TP901-1.

---

Organizational Affiliation: 

Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CI	A	83	Lactococcus phage TP901-1	Mutation(s): 2  Gene Names: cI
UniProt
Find proteins for O48503 (Lactococcus phage TP901-1) Explore O48503  Go to UniProtKB:  O48503

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.183 
• R-Value Work: 0.135 
• R-Value Observed: 0.137 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.62	α = 90
b = 43.59	β = 90
c = 71.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-21 
• Released Date: 2013-12-25 
Deposition Author(s): Frandsen, K.H., Rasmussen, K.K., Poulsen, J.N., Lo Leggio, L.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release