1nkd: Difference between revisions

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 <StructureSection load='1nkd' size='340' side='right'caption='[[1nkd]], [[Resolution|resolution]] 1.09&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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>
+<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>
-</td></tr><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>
+</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>
+<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>
 </table>
 == Function ==
-[[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.
+[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.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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:10089502<ref>PMID:10089502</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1nkd" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Rop protein|Rop protein]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Kokkinidis, M]]
+[[Category: Kokkinidis M]]
-[[Category: Vlassi, M]]
+[[Category: Vlassi M]]
-[[Category: 4-alpha-helix bundle]]
-[[Category: Atomic resolution structure]]
-[[Category: Transcription regulation]]