1QX8

Crystal structure of a five-residue deletion mutant of the Rop protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Loopless Rop: structure and dynamics of an engineered homotetrameric variant of the repressor of primer protein.

Glykos, N.M.Papanikolau, Y.Vlassi, M.Kotsifaki, D.Cesareni, G.Kokkinidis, M.

(2006) Biochemistry 45: 10905-10919

  • DOI: 10.1021/bi060833n
  • Primary Citation of Related Structures:  
    1QX8

  • PubMed Abstract: 
  • The repressor of primer (Rop) protein has become a steady source of surprises concerning the relationship between the sequences and the structures of several of its mutants and variants. Here we add another piece to the puzzle of Rop by showing that ...

    The repressor of primer (Rop) protein has become a steady source of surprises concerning the relationship between the sequences and the structures of several of its mutants and variants. Here we add another piece to the puzzle of Rop by showing that an engineered deletion mutant of the protein (corresponding to a deletion of residues 30-34 of the wild-type protein and designed to restore the heptad periodicity at the turn region) results in a complete reorganization of the bundle which is converted from a homodimer to a homotetramer. In contrast (and as previously shown), a two-residue insertion, which also restores the heptad periodicity, is essentially identical with wild-type Rop. The new deletion mutant structure is a canonical, left-handed, all-antiparallel bundle with a completely different hydrophobic core and distinct surface properties. The structure agrees and qualitatively explains the results from functional, thermodynamic, and kinetic studies which indicated that this deletion mutant is a biologically inactive hyperstable homotetramer. Additional insight into the stability and dynamics of the mutant structure has been obtained from extensive molecular dynamics simulations in explicit water and with full treatment of electrostatics.


    Related Citations: 
    • Ionic strength reducers: an efficient approach to protein purification and crystallization. Application to two Rop variants
      (2004) Acta Crystallogr D Biol Crystallogr 60: 1334

    Organizational Affiliation

    Department of Molecular Biology and Genetics, Democritus University of Thrace, Dimitras 19, 68100 Alexandroupolis, Greece.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory protein ROPAB58Escherichia coliMutation(s): 0 
Gene Names: rop
Find proteins for P03051 (Escherichia coli)
Explore P03051 
Go to UniProtKB:  P03051
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.476α = 90
b = 42.565β = 104.68
c = 51.722γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance