1flp: Difference between revisions

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-[[Image:1flp.gif|left|200px]]
-<!--
+==STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA PECTINATA: CRYSTALLOGRAPHIC ANALYSIS AT 1.5 ANGSTROMS RESOLUTION==
-The line below this paragraph, containing "STRUCTURE_1flp", creates the "Structure Box" on the page.
+<StructureSection load='1flp' size='340' side='right'caption='[[1flp]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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='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>
-{{STRUCTURE_1flp|  PDB=1flp  |  SCENE=  }}
+<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 ==
+[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>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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>
-'''STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA PECTINATA: CRYSTALLOGRAPHIC ANALYSIS AT 1.5 ANGSTROMS RESOLUTION'''
+==See Also==
+*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-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.
+[[Category: Large Structures]]
+[[Category: Phacoides pectinatus]]
-==About this Structure==
+[[Category: Ascenzi P]]
-FLP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lucina_pectinata Lucina pectinata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FLP OCA].
+[[Category: Bolognesi M]]
+[[Category: Coda A]]
-==Reference==
+[[Category: Fasano M]]
-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:[http://www.ncbi.nlm.nih.gov/pubmed/7966324 7966324]
+[[Category: Rizzi M]]
-[[Category: Lucina pectinata]]
+[[Category: Wittenberg JB]]
-[[Category: Single protein]]
-[[Category: Ascenzi, P.]]
-[[Category: Bolognesi, M.]]
-[[Category: Coda, A.]]
-[[Category: Fasano, M.]]
-[[Category: Rizzi, M.]]
-[[Category: Wittenberg, J B.]]
-[[Category: Oxygen transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 16:28:35 2008''