1LMB

REFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OPERATOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Refined 1.8 A crystal structure of the lambda repressor-operator complex.

Beamer, L.J.Pabo, C.O.

(1992) J Mol Biol 227: 177-196

  • DOI: 10.1016/0022-2836(92)90690-l
  • Primary Citation of Related Structures:  
    1LMB

  • PubMed Abstract: 
  • The crystal structure of the lambda repressor-operator complex has been refined to an R-factor of 18.9% at 1.8 A resolution. This refinement, using data collected at low temperature, has revealed the structure of the N-terminal arm and shows that the interactions of repressor with the two halves of the pseudo-symmetric operator site are significantly different ...

    The crystal structure of the lambda repressor-operator complex has been refined to an R-factor of 18.9% at 1.8 A resolution. This refinement, using data collected at low temperature, has revealed the structure of the N-terminal arm and shows that the interactions of repressor with the two halves of the pseudo-symmetric operator site are significantly different. The two halves of the complex are most similar near the outer edge of the operator site (in a region where the lambda and 434 repressors make similar contacts), but they become increasingly different toward the center of the operator. There are striking differences near the center of the site where it appears that the arm makes significant contacts to only one half of the DNA site. This suggested a new way of aligning the operator sites in phage lambda. The high resolution structure confirms many of the previously noted features of the complex, but also reveals a number of new protein-DNA contacts. It also gives a better view of the extensive H-bonding networks that couple contacts made by different residues and different regions of the protein, and reveals important new details about the helix-turn-helix (HTH) region, and the positions of many water molecules in the complex.


    Related Citations: 
    • The DNA Binding Arm of a Lambda Repressor: Critical Contacts from a Flexible Region
      Clarke, N.D., Beamer, L.J., Goldberg, H.R., Berkower, C., Pabo, C.O.
      (1991) Science 254: 267
    • Conserved Residues Make Similar Contacts in Two Repressor-Operator Complexes
      Pabo, C.O., Aggarwal, A.K., Jordan, S.R., Beamer, L.J., Obeysekare, U.R., Harrison, S.C.
      (1990) Science 247: 1210
    • Comparison of the Structures of Cro and Lambda Repressor Proteins from Bacteriophage Lambda
      Ohlendorf, D.H., Anderson, W.F., Lewis, M., Pabo, C.O., Matthews, B.W.
      (1983) J Mol Biol 169: 757
    • Structure of the Operator-Binding Domain of Bacteriophage Lambda Repressor. Implications for DNA Recognition and Gene Regulation
      Lewis, M., Jeffrey, A., Wang, J., Ladner, R., Ptashne, M., Pabo, C.O.
      (1983) Cold Spring Harb Symp Quant Biol 47: 435
    • Homology Among DNA-Binding Proteins Suggests Use of a Conserved Super-Secondary Structure
      Sauer, R.T., Yocum, R.R., Doolittle, R.F., Lewis, M., Pabo, C.O.
      (1982) Nature 298: 447
    • The Operator-Binding Domain of Lambda Repressor. Structure and DNA Recognition
      Pabo, C.O., Lewis, M.
      (1982) Nature 298: 443
    • The N-Terminal Arms of Lambda Repressor Wrap Around the Operator DNA
      Pabo, C.O., Krovatin, W., Jeffrey, A., Sauer, R.T.
      (1982) Nature 298: 441

    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (LAMBDA REPRESSOR)C [auth 3], D [auth 4]92Escherichia virus LambdaMutation(s): 0 
Gene Names: cIlambdap88
UniProt
Find proteins for P03034 (Escherichia phage lambda)
Explore P03034 
Go to UniProtKB:  P03034
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3')A [auth 1]20N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3')B [auth 2]20N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.80 Å
      • R-Value Work: 0.189 
      • R-Value Observed: 0.189 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 37.22α = 90
      b = 68.72β = 92.2
      c = 57.03γ = 90
      Software Package:
      Software NamePurpose
      X-PLORrefinement
      TNTrefinement

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 1991-11-05 
      • Released Date: 1991-11-05 
      • Deposition Author(s): Beamer, L.J., Pabo, C.O.
      • This entry supersedes: 1LRD

      Revision History  (Full details and data files)

      • Version 1.0: 1991-11-05
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance