1NKD

ATOMIC RESOLUTION (1.07 ANGSTROMS) STRUCTURE OF THE ROP MUTANT <2AA>


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.134 
  • R-Value Observed: 0.104 

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This is version 1.3 of the entry. See complete history


Literature

Structural parameters for proteins derived from the atomic resolution (1.09 A) structure of a designed variant of the ColE1 ROP protein.

Vlassi, M.Dauter, Z.Wilson, K.S.Kokkinidis, M.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1245-1260

  • DOI: 10.1107/s0907444998002492
  • Primary Citation of Related Structures:  
    1NKD

  • PubMed Abstract: 
  • The crystal structure of a designed variant of the ColE1 repressor of primer (ROP) protein has been refined with SHELXL93 to a resolution of 1.09 A. The final model with 510 non-H protein atoms, 576 H atoms in calculated positions and 114 water molecules converged to a standard R factor of 10% using unrestrained blocked full-matrix refinement ...

    The crystal structure of a designed variant of the ColE1 repressor of primer (ROP) protein has been refined with SHELXL93 to a resolution of 1.09 A. The final model with 510 non-H protein atoms, 576 H atoms in calculated positions and 114 water molecules converged to a standard R factor of 10% using unrestrained blocked full-matrix refinement. For all non-H atoms six-parameter anisotropic thermal parameters have been refined. The majority of atomic vibrations have a preferred orientation which is approximately perpendicular to the bundle axis; analysis with the TLS method [Schomaker & Trueblood (1968). Acta Cryst. B24, 63-77] showed a relatively good agreement between the individual atomic displacements and a rigid-body motion of the protein. Disordered residues with multiple conformations form clusters on the surface of the protein; six C-terminal residues have been omitted from the refined model due to disorder. Part of the solvent structure forms pentagonal or hexagonal clusters which bridge neighbouring protein molecules. Some water molecules are also conserved in wild-type ROP. The unrestrained blocked full-matrix least-squares refinement yielded reliable estimates of the standard deviations of the refined parameters. Comparison of these parameters with the stereochemical restraints used in various protein refinement programs showed statistically significant differences. These restraints should be adapted to the refinement of macromolecules by taking into account parameters determined from atomic resolution protein structures.


    Related Citations: 
    • Restored Heptad Pattern Continuity Does not Alter the Folding of a Four-Alpha-Helix Bundle
      Vlassi, M., Steif, C., Weber, P., Tsernoglou, D., Wilson, K.S., Hinz, H.J., Kokkinidis, M.
      (1994) Nat Struct Biol 1: 706
    • Correlation between Protein Stability and Crystal Properties of Designed Rop Variants
      Kokkinidis, M., Vlassi, M., Papanikolaou, Y., Kotsifaki, D., Kingswell, A., Tsernoglou, D., Hinz, H.J.
      (1993) Proteins 16: 214
    • Structure of the Cole1 Rop Protein at 1.7 A Resolution
      Banner, D.W., Kokkinidis, M., Tsernoglou, D.
      (1987) J Mol Biol 196: 657

    Organizational Affiliation

    National Centre for Scientific Research 'DEMOCRITOS', 15310 Ag. Paraskevi-Attikis, Athens, Greece.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ROPA65Escherichia coliMutation(s): 0 
Gene Names: rop
UniProt
Find proteins for P03051 (Escherichia coli)
Explore P03051 
Go to UniProtKB:  P03051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03051
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.134 
  • R-Value Observed: 0.104 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.06α = 90
b = 37.88β = 100.8
c = 31.65γ = 90
Software Package:
Software NamePurpose
SHELXL-93model building
SHELXL-93refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other