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1rwy

From Proteopedia

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[[Image:1rwy.gif|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN AT 1.05 RESOLUTION==
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|PDB= 1rwy |SIZE=350|CAPTION= <scene name='initialview01'>1rwy</scene>, resolution 1.05&Aring;
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<StructureSection load='1rwy' size='340' side='right'caption='[[1rwy]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1rwy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RWY FirstGlance]. <br>
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|ACTIVITY=
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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]] 1.05&#8491;</td></tr>
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|GENE= PVALB, PVA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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|DOMAIN=
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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=1rwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwy OCA], [https://pdbe.org/1rwy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rwy RCSB], [https://www.ebi.ac.uk/pdbsum/1rwy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rwy ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1rtp|1RTP]], [[1g33|1G33]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwy OCA], [http://www.ebi.ac.uk/pdbsum/1rwy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rwy RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/PRVA_RAT PRVA_RAT] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.
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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/rw/1rwy_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=1rwy ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of rat alpha-parvalbumin has been determined at 1.05 Angstrom resolution, using synchrotron data collected at Advanced Photon Source beamline 19-ID. After refinement with SHELX, employing anisotropic displacement parameters and riding hydrogen atoms, R = 0.132 and R(free) = 0.162. The average coordinate estimated standard deviations are 0.021 Angstrom and 0.038 Angstrom for backbone atoms and side-chain atoms, respectively. Besides providing a more precise view of the alpha-isoform than previously available, these data permit comparison with the 0.91 Angstrom structure determined for pike beta-parvalbumin. Visualization of the anisotropic displacement parameters as thermal ellipsoids yields insight into the atomic motion within the Ca(2+)-binding sites. The asymmetric unit includes three parvalbumin (PV) molecules. Interestingly, the EF site in one displays uncharacteristic flexibility. The ellipsoids for Asp-92 are particularly large and non-spherical, and the shape of the Ca(2+) ellipsoid implies significant vibrational motion perpendicular to the plane defined by the four y and z ligands. The relative dearth of crystal-packing interactions in this site suggests that the heightened flexibility may be the result of diminished intermolecular contacts. The implication is that, by impeding conformational mobility, crystal-packing forces may cause serious overestimation of EF-hand rigidity. The high quality of the data permitted 11 residues to be modeled in alternative side-chain conformations, including the two core residues, Ile-97 and Leu-105. The discrete disorder observed for Ile-97 may have functional ramifications, providing a mechanism for communicating binding status between the CD and EF binding loops and between the PV metal ion-binding domain and the N-terminal AB region.
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'''CRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN AT 1.05 RESOLUTION'''
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Crystal structure of rat alpha-parvalbumin at 1.05 Angstrom resolution.,Bottoms CA, Schuermann JP, Agah S, Henzl MT, Tanner JJ Protein Sci. 2004 Jul;13(7):1724-34. Epub 2004 May 28. PMID:15169955<ref>PMID:15169955</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1rwy" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The crystal structure of rat alpha-parvalbumin has been determined at 1.05 Angstrom resolution, using synchrotron data collected at Advanced Photon Source beamline 19-ID. After refinement with SHELX, employing anisotropic displacement parameters and riding hydrogen atoms, R = 0.132 and R(free) = 0.162. The average coordinate estimated standard deviations are 0.021 Angstrom and 0.038 Angstrom for backbone atoms and side-chain atoms, respectively. Besides providing a more precise view of the alpha-isoform than previously available, these data permit comparison with the 0.91 Angstrom structure determined for pike beta-parvalbumin. Visualization of the anisotropic displacement parameters as thermal ellipsoids yields insight into the atomic motion within the Ca(2+)-binding sites. The asymmetric unit includes three parvalbumin (PV) molecules. Interestingly, the EF site in one displays uncharacteristic flexibility. The ellipsoids for Asp-92 are particularly large and non-spherical, and the shape of the Ca(2+) ellipsoid implies significant vibrational motion perpendicular to the plane defined by the four y and z ligands. The relative dearth of crystal-packing interactions in this site suggests that the heightened flexibility may be the result of diminished intermolecular contacts. The implication is that, by impeding conformational mobility, crystal-packing forces may cause serious overestimation of EF-hand rigidity. The high quality of the data permitted 11 residues to be modeled in alternative side-chain conformations, including the two core residues, Ile-97 and Leu-105. The discrete disorder observed for Ile-97 may have functional ramifications, providing a mechanism for communicating binding status between the CD and EF binding loops and between the PV metal ion-binding domain and the N-terminal AB region.
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*[[Parvalbumin|Parvalbumin]]
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== References ==
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==About this Structure==
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<references/>
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1RWY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWY OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Crystal structure of rat alpha-parvalbumin at 1.05 Angstrom resolution., Bottoms CA, Schuermann JP, Agah S, Henzl MT, Tanner JJ, Protein Sci. 2004 Jul;13(7):1724-34. Epub 2004 May 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15169955 15169955]
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Agah S]]
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[[Category: Agah, S.]]
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[[Category: Bottoms CA]]
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[[Category: Bottoms, C A.]]
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[[Category: Henzl MT]]
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[[Category: Henzl, M T.]]
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[[Category: Schuermann JP]]
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[[Category: Schuermann, J P.]]
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[[Category: Tanner JJ]]
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[[Category: Tanner, J J.]]
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[[Category: calcium-binding]]
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[[Category: ef-hand]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:34:06 2008''
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Current revision

CRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN AT 1.05 RESOLUTION

PDB ID 1rwy

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