1NKD

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

1NKD の概要

• エントリーDOI: 10.2210/pdb1nkd/pdb
• 分子名称: ROP (2 entities in total)
• 機能のキーワード: rop (cole1 repressor of primer), atomic resolution structure, 4-alpha-helix bundle, transcription regulation
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 7379.19

構造登録者

Vlassi, M.,Kokkinidis, M. (登録日: 1997-09-23, 公開日: 1999-03-23, 最終更新日: 2024-02-14)

主引用文献

Vlassi, M.,Dauter, Z.,Wilson, K.S.,Kokkinidis, M.
Structural parameters for proteins derived from the atomic resolution (1.09 A) structure of a designed variant of the ColE1 ROP protein.
Acta Crystallogr.,Sect.D, 54:1245-1260, 1998

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. 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.

PubMed: 10089502
DOI: 10.1107/S0907444998002492

実験手法

X-RAY DIFFRACTION (1.09 Å)