PDBsum entry 1nkd

Transcription regulation

PDB id: 1nkd

Contents

Protein chain

59 a.a. *

Waters ×114

* Residue conservation analysis

PDB id:

1nkd

Name:

Transcription regulation

Title:

Atomic resolution (1.07 angstroms) structure of the rop mutant <2aa>

Structure:

Rop. Chain: a. Synonym: cole1 repressor of primer. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

1.09Å R-factor: 0.101 R-free: 0.134

Authors:

M.Vlassi,M.Kokkinidis

Key ref:

M.Vlassi et al. (1998). Structural parameters for proteins derived from the atomic resolution (1.09 A) structure of a designed variant of the ColE1 ROP protein. Acta Crystallogr D Biol Crystallogr, 54, 1245-1260. PubMed id: 10089502 DOI: 10.1107/S0907444998002492

Date:

23-Sep-97 Release date: 23-Mar-99

Protein chain

P03051  (ROP_ECOLX) -  Regulatory protein rop from Escherichia coli

Seq: 63 a.a.

Struc: 59 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1107/S0907444998002492

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

PubMed id: 10089502

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

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

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.

Selected figure(s)

Figure 1.
Figure 1 Schematic representation of the structure of aa}\rangle] .

Figure 2.
Figure 2 Course of the R factors during the refinement of aa}\rangle] .

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1998, 54, 1245-1260) copyright 1998.

Figures were selected by an automated process.