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 

wwPDB Validation 3D Report Full Report


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.,Sect.D 54: 1245-1260


  • 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 molec ...

    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: 
    • 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
    • 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.Mol.Biol. 1: 706
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ROP
A
65Escherichia coliGene Names: rop
Find proteins for P03051 (Escherichia coli)
Go to UniProtKB:  P03051
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.134 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 47.060α = 90.00
b = 37.880β = 100.80
c = 31.650γ = 90.00
Software Package:
Software NamePurpose
SHELXL-93refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93phasing
SHELXL-93model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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