2OR1

RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VIEW AT HIGH RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2OR1/pdb
• NAKB: 2OR1

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


• Deposited: 1989-09-05 Released: 1989-09-05 
• Deposition Author(s): Aggarwal, A.K., Rodgers, D.W., Drottar, M., Ptashne, M., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 0.179 

Literature

Recognition of a DNA operator by the repressor of phage 434: a view at high resolution.

Aggarwal, A.K., Rodgers, D.W., Drottar, M., Ptashne, M., Harrison, S.C.

(1988) Science 242: 899-907

• PubMed: 3187531 
• DOI: https://doi.org/10.1126/science.3187531
• Primary Citation of Related Structures:  
  2OR1


• PubMed Abstract: 
  

  The repressors of temperate bacteriophages such as 434 and lambda control transcription by binding to a set of DNA operator sites. The different affinity of repressor for each of these sites ensures efficient regulation. High-resolution x-ray crystallography was used to study the DNA-binding domain of phage 434 repressor in complex with a synthetic DNA operator. The structure shows recognition of the operator by direct interactions with base pairs in the major groove, combined with the sequence-dependent ability of DNA to adopt the required conformation on binding repressor. In particular, a network of three-centered bifurcated hydrogen bonds among base pairs in the operator helps explain why 434 repressor prefers certain sites over others. These bonds, which stabilize the conformation of the bound DNA, can form only with certain sequences.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, 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: 1,826 
• 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
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*AP*AP*CP*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*GP*TP*TP*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: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.3	α = 90
b = 65	β = 90
c = 27.7	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1989-09-05 
Deposition Author(s): Aggarwal, A.K., Rodgers, D.W., Drottar, M., Ptashne, M., Harrison, S.C.

Revision History  

• Version 1.0: 1989-09-05
  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: 2024-02-21
  Changes: Data collection, Database references