1nkd

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(New page: 200px<br /><applet load="1nkd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nkd, resolution 1.09&Aring;" /> '''ATOMIC RESOLUTION (1...)
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[[Image:1nkd.gif|left|200px]]<br /><applet load="1nkd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nkd, resolution 1.09&Aring;" />
 
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'''ATOMIC RESOLUTION (1.07 ANGSTROMS) STRUCTURE OF THE ROP MUTANT <2AA>'''<br />
 
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==Overview==
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==ATOMIC RESOLUTION (1.07 ANGSTROMS) STRUCTURE OF THE ROP MUTANT <2AA>==
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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 &amp; 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.
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<StructureSection load='1nkd' size='340' side='right'caption='[[1nkd]], [[Resolution|resolution]] 1.09&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1nkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NKD FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.09&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkd OCA], [https://pdbe.org/1nkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nkd RCSB], [https://www.ebi.ac.uk/pdbsum/1nkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ROP_ECOLX ROP_ECOLX] Regulates plasmid DNA replication by modulating the initiation of transcription of the primer RNA precursor. Processing of the precursor of the primer, RNAII, is inhibited by hydrogen bonding of RNAII to its complementary sequence in RNAI. ROP increases the affinity of RNAI for RNAII and thus decreases the rate of replication initiation events.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nk/1nkd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nkd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1NKD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NKD OCA].
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*[[Rop protein|Rop protein]]
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__TOC__
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==Reference==
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</StructureSection>
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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 KS, Kokkinidis M, Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1245-60. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10089502 10089502]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Kokkinidis, M.]]
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[[Category: Kokkinidis M]]
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[[Category: Vlassi, M.]]
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[[Category: Vlassi M]]
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[[Category: 4-alpha-helix bundle]]
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[[Category: atomic resolution structure]]
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[[Category: rop (cole1 repressor of primer)]]
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[[Category: transcription regulation]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:19:55 2007''
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Current revision

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

PDB ID 1nkd

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