2OVG

Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two structures of a lambda Cro variant highlight dimer flexibility but disfavor major dimer distortions upon specific binding of cognate DNA.

Hall, B.M.Roberts, S.A.Heroux, A.Cordes, M.H.

(2008) J Mol Biol 375: 802-811

  • DOI: 10.1016/j.jmb.2007.10.082
  • Primary Citation of Related Structures:  
    2ECS, 2OVG

  • PubMed Abstract: 
  • Previously reported crystal structures of free and DNA-bound dimers of lambda Cro differ strongly (about 4 A backbone rmsd), suggesting both flexibility of the dimer interface and induced-fit protein structure changes caused by sequence-specific DNA binding ...

    Previously reported crystal structures of free and DNA-bound dimers of lambda Cro differ strongly (about 4 A backbone rmsd), suggesting both flexibility of the dimer interface and induced-fit protein structure changes caused by sequence-specific DNA binding. Here, we present two crystal structures, in space groups P3(2)21 and C2 at 1.35 and 1.40 A resolution, respectively, of a variant of lambda Cro with three mutations in its recognition helix (Q27P/A29S/K32Q, or PSQ for short). One dimer structure (P3(2)21; PSQ form 1) resembles the DNA-bound wild-type Cro dimer (1.0 A backbone rmsd), while the other (C2; PSQ form 2) resembles neither unbound (3.6 A) nor bound (2.4 A) wild-type Cro. Both PSQ form 2 and unbound wild-type dimer crystals have a similar interdimer beta-sheet interaction between the beta1 strands at the edges of the dimer. In the former, an infinite, open beta-structure along one crystal axis results, while in the latter, a closed tetrameric barrel is formed. Neither the DNA-bound wild-type structure nor PSQ form 1 contains these interdimer interactions. We propose that beta-sheet superstructures resulting from crystal contact interactions distort Cro dimers from their preferred solution conformation, which actually resembles the DNA-bound structure. These results highlight the remarkable flexibility of lambda Cro but also suggest that sequence-specific DNA binding may not induce large changes in the protein structure.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phage lambda CroA66Escherichia virus LambdaMutation(s): 3 
Gene Names: crolambdap57
UniProt
Find proteins for P03040 (Escherichia phage lambda)
Explore P03040 
Go to UniProtKB:  P03040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03040
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
C [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.524α = 90
b = 50.524β = 90
c = 48.148γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations