1flp: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA PECTINATA: CRYSTALLOGRAPHIC ANALYSIS AT 1.5 ANGSTROMS RESOLUTION==
-<StructureSection load='1flp' size='340' side='right' caption='[[1flp]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='1flp' size='340' side='right'caption='[[1flp]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1flp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FLP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FLP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1flp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phacoides_pectinatus Phacoides pectinatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FLP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.5&#8491;</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=1flp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1flp OCA], [http://pdbe.org/1flp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1flp RCSB], [http://www.ebi.ac.uk/pdbsum/1flp PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=1flp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1flp OCA], [https://pdbe.org/1flp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1flp RCSB], [https://www.ebi.ac.uk/pdbsum/1flp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1flp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GLB1_PHAPT GLB1_PHAPT]] Serves to transport hydrogen sulfide to autotrophic bacteria.
+[https://www.uniprot.org/uniprot/GLB1_PHAPT GLB1_PHAPT] Serves to transport hydrogen sulfide to autotrophic bacteria.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fl/1flp_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fl/1flp_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / Line 20: @@
 </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=1flp ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of the aquo-met form of the sulfide-reactive hemoglobin (component I) from the gill of the symbiont-harboring mollusc, Lucina pectinata, has been solved and refined at 1.5 A resolution, based on synchrotron radiation X-ray diffraction data, and employing molecular replacement techniques. The crystallographic R-factor, calculated for the data in the 15.0 to 1.5 A resolution range, is 0.170, with highly regular stereochemical parameters for the protein model, and including 131 water molecules. The monomeric hemoglobin I chain consists of 142 amino acid residues, which have been partly identified on the basis of the crystallographic analysis. The molecule is characterized by an unusual distribution of aromatic residues, particularly in the region surrounding the distal site in the heme pocket. The heme distal residue is Gln(64)E7, while other notable amino acid substitutions include Trp(21)B2, Phe(29)B10, Leu(46)CD3, Phe(68)E11 and Trp(75)E18. An amino acid insertion (Ser44) is observed between sites CD1 and CD2. In the aquo-met protein, a water molecule is present at the sixth coordination position of the heme iron, and hydrogen bonded to Gln(64)E7. Simple model building shows that a dioxygen molecule, bound to ferrous protein, would contact with its free atom the ring edge of Phe(29)B10, being thus stabilized at the coordination site by an aromatic-electrostatic interaction. Similarly, the unique packing and organization of aromatic residues in the surroundings of the heme distal site is proposed as the molecular basis of the very high affinity of Lucina pectinata hemoglobin I for hydrogen sulfide, considered as one of the two physiological ligands of the protein.
-Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata. Crystallographic analysis at 1.5 A resolution.,Rizzi M, Wittenberg JB, Coda A, Fasano M, Ascenzi P, Bolognesi M J Mol Biol. 1994 Nov 18;244(1):86-99. PMID:7966324<ref>PMID:7966324</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1flp" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Ascenzi, P]]
+[[Category: Large Structures]]
-[[Category: Bolognesi, M]]
+[[Category: Phacoides pectinatus]]
-[[Category: Coda, A]]
+[[Category: Ascenzi P]]
-[[Category: Fasano, M]]
+[[Category: Bolognesi M]]
-[[Category: Rizzi, M]]
+[[Category: Coda A]]
-[[Category: Wittenberg, J B]]
+[[Category: Fasano M]]
-[[Category: Oxygen transport]]
+[[Category: Rizzi M]]
+[[Category: Wittenberg JB]]