1PER

THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES

• PDB DOI: https://doi.org/10.2210/pdb1PER/pdb
• NAKB: 1PER

• Classification: TRANSCRIPTION/DNA
• Organism(s): Phage 434
• Mutation(s): No 


• Deposited: 1993-11-09 Released: 1994-01-31 
• Deposition Author(s): Rodgers, D.W., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 0.187 

Literature

The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.

Rodgers, D.W., Harrison, S.C.

(1993) Structure 1: 227-240

• PubMed: 8081737 
• DOI: https://doi.org/10.1016/0969-2126(93)90012-6
• Primary Citation of Related Structures:  
  1PER


• PubMed Abstract: 
  

  The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. OR3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138.

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: 27.38 kDa 
• Atom Count: 1,822 
• Modelled Residue Count: 166 
• Deposited Residue Count: 178 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (434 REPRESSOR)	C [auth L], D [auth R]	69	Phage 434	Mutation(s): 0
UniProt
Find proteins for P16117 (Enterobacteria phage 434) Explore P16117  Go to UniProtKB:  P16117

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*GP*TP*TP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3')	A	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*AP*AP*CP*TP*GP*T P*AP*CP*T)-3')	B	20	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.9	α = 90
b = 64.5	β = 90
c = 27.8	γ = 90

Software Package:

Software Name	Purpose
CORELS	refinement
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Rodgers, D.W., Harrison, S.C.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references