1ab1: Difference between revisions

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-[[Image:1ab1.gif|left|200px]]
-<!--
+==SI FORM CRAMBIN==
-The line below this paragraph, containing "STRUCTURE_1ab1", creates the "Structure Box" on the page.
+<StructureSection load='1ab1' size='340' side='right'caption='[[1ab1]], [[Resolution|resolution]] 0.89&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'>[[1ab1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Crambe_hispanica_subsp._abyssinica Crambe hispanica subsp. abyssinica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AB1 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]] 0.89&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene></td></tr>
-{{STRUCTURE_1ab1|  PDB=1ab1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ab1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ab1 OCA], [https://pdbe.org/1ab1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ab1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ab1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ab1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CRAM_CRAAB CRAM_CRAAB] The function of this hydrophobic plant seed protein is not known.
+== 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/ab/1ab1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ab1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+It is not agreed that correlated positions of disordered protein side chains (substate correlations) can be deduced from diffraction data. The pure Ser-22/Ile-25 (SI form) crambin crystal structure confirms correlations deduced for the natural, mixed sequence form of crambin crystals. Physical separation of the mixed form into pure SI form and Pro-22/Leu-25 (PL form) crambin and the PL form crystal structure determination (Yamano, A., and Teeter, M. M. (1994) J. Biol. Chem. 269, 13956-13965) support the proposed (Teeter, M. M., Roe, S. M., and Heo, N. H. (1993) J. Mol. Biol. 230, 292-311) correlation model. Electron density of mixed form crambin crystals shows four possible pairs of side chain conformations for heterogeneous residue 22 and nearby Tyr-29 (2(2) = 4, two conformations for each of two side chains). One combination can be eliminated because of short van der Waals' contacts. However, only two alternates have been postulated to exist in mixed form crambin: Pro-22/Tyr-29A and Ser-22/Tyr-29B. In crystals of the PL form, Pro-22 and Tyr-29A are found to be in direct van der Waals' contact (Yamano, A., and Teeter, M. M. (1994) J. Biol. Chem. 269, 13956-13965). Comparison of the SI form structure with the mixed form electron density confirms that the fourth combination of side chains does not occur and that side chain correlations are mediated by water networks.
-'''SI FORM CRAMBIN'''
+Crystal structure of Ser-22/Ile-25 form crambin confirms solvent, side chain substate correlations.,Yamano A, Heo NH, Teeter MM J Biol Chem. 1997 Apr 11;272(15):9597-600. PMID:9092482<ref>PMID:9092482</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==Overview==
+</div>
-To enhance the already high quality of diffraction data for crystals of the hydrophobic protein crambin, X-ray data were collected at 130 K by the method of H. Hope to 0.83 A resolution. Refinement with PROLSQ yields a model with an R value of 10.5%. The final model had three parameter anisotropic vibration factors for all atoms, which included 367 protein heavy atoms, 372 hydrogen atoms and 144 solvent atoms with one ethanol molecule. Dihedral angles and hydrogen-bonding distances generally agree with earlier studies of high-resolution protein structures, but some new patterns are noted. Solvent-related helix distortions are reminiscent of those described by others. Helix and beta-sheet regions show distinct patterns in their side-chain conformations. Despite crambin's hydrophobic nature, its accessible surface area in the crystal is surprisingly close to that of water-soluble proteins like myoglobin and carboxypeptidase A. More of crambin's hydrophobic surface is buried in the crystal, perhaps accounting for its high order of diffraction. A total of 24% of the 46 residues show discrete disorder at 130 K. This includes five side-chains at both 300 and 130 K, and six more side-chains and an ethanol molecule at 130 K. Disorder is associated with the sequence microheterogeneity at Pro/Ser22 and Leu/Ile25, with space filling or with solvent disorder. Correlated conformations extend over three to five residues. The patterns of disorder in this structure reveal important principles of protein structure and its dynamics. Finding disordered groups correlated over 5 to 8 A suggests that co-ordinated motion extends in groups rather than simply as uncorrelated movement around an atom center. Thermal diffuse scattering experiments on insulin and lysozyme are consistent with this interpretation. Nearly all of the protein-bound solvent has been located. Less than 1% of protein accessible surface area remains uncovered by solvent or crystal contacts. Preliminary analysis of the solvent network reveals two main networks in each of four solvent regions.
+<div class="pdbe-citations 1ab1" style="background-color:#fffaf0;"></div>
+== References ==
-==About this Structure==
+<references/>
-AB1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Crambe_hispanica_subsp._abyssinica Crambe hispanica subsp. abyssinica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AB1 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Atomic resolution (0.83 A) crystal structure of the hydrophobic protein crambin at 130 K., Teeter MM, Roe SM, Heo NH, J Mol Biol. 1993 Mar 5;230(1):292-311. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8450543 8450543]
 [[Category: Crambe hispanica subsp. abyssinica]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Teeter, M M.]]
+[[Category: Teeter MM]]
-[[Category: Yamano, A.]]
+[[Category: Yamano A]]
-[[Category: Plant seed protein]]
-[[Category: Thionin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 10:03:37 2008''