1f4m: Difference between revisions

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<StructureSection load='1f4m' size='340' side='right'caption='[[1f4m]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
<StructureSection load='1f4m' size='340' side='right'caption='[[1f4m]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1f4m]] is a 6 chain structure with sequence from [http://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=1F4M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F4M FirstGlance]. <br>
<table><tr><td colspan='2'>[[1f4m]] is a 6 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=1F4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F4M FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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]] 2.25&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1f4n|1f4n]], [[1rop|1rop]], [[1gto|1gto]], [[1nkd|1nkd]], [[1rpo|1rpo]], [[1b6q|1b6q]], [[1rpr|1rpr]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f4m OCA], [http://pdbe.org/1f4m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f4m RCSB], [http://www.ebi.ac.uk/pdbsum/1f4m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f4m ProSAT]</span></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=1f4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f4m OCA], [https://pdbe.org/1f4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f4m RCSB], [https://www.ebi.ac.uk/pdbsum/1f4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f4m ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[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=1f4m ConSurf].
</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=1f4m ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Rop is an RNA binding, dimeric, four-helix bundle protein with a well-defined, regular hydrophobic core ideally suited for redesign studies. A family of Rop variants in which the hydrophobic core was systematically redesigned has previously been created and characterized. RESULTS: We present a structural and thermodynamic analysis of Ala2Ile2-6, a variant of Rop with an extensively redesigned hydrophobic core. The structure of Ala2Ile2-6 reveals a completely new fold formed by a conformational "flip" of the two protomers around the dimeric interface. The free-energy profile of Ala2Ile2-6 is also very different from that of wild-type Rop. Ala2Ile2-6 has a higher melting temperature than Rop, but undergoes a slightly smaller free-energy change on unfolding. CONCLUSIONS: The structure of Ala2Ile2-6, along with molecular modeling results, demonstrate the importance of tight packing of core residues and the adoption of favorable core side chain rotamer values in determining helix-helix interactions in the four-helix bundle fold. Structural disorder at the N and C termini of Ala2Ile2-6 provides a basis for the large differences in the enthalpy and entropy of Ala2Ile2-6 folding compared with wildtype Rop.
Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core.,Willis MA, Bishop B, Regan L, Brunger AT Structure. 2000 Dec 15;8(12):1319-28. PMID:11188696<ref>PMID:11188696</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1f4m" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Rop protein|Rop protein]]
*[[Rop protein|Rop protein]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bishop, B]]
[[Category: Bishop B]]
[[Category: Brunger, A T]]
[[Category: Brunger AT]]
[[Category: Regan, L]]
[[Category: Regan L]]
[[Category: Willis, M A]]
[[Category: Willis MA]]
[[Category: Dimer]]
[[Category: Helix-turn-helix]]
[[Category: Homodimer]]
[[Category: Hydrophobic core packing]]
[[Category: Rop]]
[[Category: Thermodynamic stability]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
Retrieved from "https://proteopedia.org/1f4m"