1ezp: Difference between revisions

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 ==GLOBAL FOLD OF MALTODEXTRIN BINDING PROTEIN COMPLEXED WITH BETA-CYCLODEXTRIN USING PEPTIDE ORIENTATIONS FROM DIPOLAR COUPLINGS==
-<StructureSection load='1ezp' size='340' side='right'caption='[[1ezp]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<StructureSection load='1ezp' size='340' side='right'caption='[[1ezp]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ezp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EZP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ezp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EZP FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ezo|1ezo]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1ezp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ezp OCA], [https://pdbe.org/1ezp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ezp RCSB], [https://www.ebi.ac.uk/pdbsum/1ezp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ezp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
+[https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
 == Evolutionary Conservation ==
 [[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=1ezp ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The global fold of maltose-binding protein in complex with the substrate beta-cyclodextrin was determined by solution NMR methods. The two-domain protein is comprised of a single polypeptide chain of 370 residues, with a molecular mass of 42 kDa. Distance information in the form of H(N)-H(N), H(N)-CH(3) and CH(3)-CH(3) NOEs was recorded on (15)N, (2)H and (15)N, (13)C, (2)H-labeled proteins with methyl protonation in Val, Leu, and Ile (C(delta1) only) residues. Distances to methyl protons, critical for the structure determination, comprised 77 % of the long-range restraints. Initial structures were calculated on the basis of 1943 NOEs, 48 hydrogen bond and 555 dihedral angle restraints. A global pair-wise backbone rmsd of 5.5 A was obtained for these initial structures with rmsd values for the N and C domains of 2.4 and 3.8 A, respectively. Direct refinement against one-bond (1)H(N)-(15)N, (13)C(alpha)-(13)CO, (15)N-(13)CO, two-bond (1)H(N)-(13)CO and three-bond (1)H(N)-(13)C(alpha) dipolar couplings resulted in structures with large numbers of dipolar restraint violations. As an alternative to direct refinement against measured dipolar couplings we have developed an approach where discrete orientations are calculated for each peptide plane on the basis of the dipolar couplings described above. The orientation which best matches that in initial NMR structures calculated from NOE and dihedral angle restraints exclusively is used to refine further the structures using a new module written for CNS. Modeling studies from four different proteins with diverse structural motifs establishes the utility of the methodology. When applied to experimental data recorded on MBP the precision of the family of structures generated improves from 5.5 to 2.2 A, while the rmsd with respect to the X-ray structure (1dmb) is reduced from 5.1 to 3.3 A.
-Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein.,Mueller GA, Choy WY, Yang D, Forman-Kay JD, Venters RA, Kay LE J Mol Biol. 2000 Jun 30;300(1):197-212. PMID:10864509<ref>PMID:10864509</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ezp" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Maltose-binding protein 3D structures|Maltose-binding protein 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Choy, W Y]]
+[[Category: Choy WY]]
-[[Category: Forman-Kay, J D]]
+[[Category: Forman-Kay JD]]
-[[Category: Kay, L E]]
+[[Category: Kay LE]]
-[[Category: Mueller, G A]]
+[[Category: Mueller GA]]
-[[Category: Venters, R A]]
+[[Category: Venters RA]]
-[[Category: Yang, D]]
+[[Category: Yang D]]
-[[Category: Deuteration]]
-[[Category: Methyl labeling]]
-[[Category: Residual diplar coupling]]
-[[Category: Sugar binding protein]]