5vf5
From Proteopedia
(Difference between revisions)
| Line 4: | Line 4: | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5vf5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_melongena Solanum melongena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VF5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[5vf5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_melongena Solanum melongena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VF5 FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.49Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5vf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vf5 OCA], [https://pdbe.org/5vf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vf5 RCSB], [https://www.ebi.ac.uk/pdbsum/5vf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vf5 ProSAT]</span></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=5vf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vf5 OCA], [https://pdbe.org/5vf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vf5 RCSB], [https://www.ebi.ac.uk/pdbsum/5vf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vf5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A0A2R2JFS1_SOLME A0A2R2JFS1_SOLME] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| - | + | The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe. The occurrence of severe errors or gross misinterpretations raises fundamental questions: Why do such aberrations emerge in the first place? How did they evade the sophisticated validation procedures which often produce clear and dire warnings, and why were severe errors not noticed by the depositors themselves, their supervisors, referees, and editors? Once detected, what can be done to either correct, improve, or eliminate such models? How do incorrect models affect the underlying claims or biomedical hypotheses they were intended, but failed, to support? What is the long-range effect of the propagation of such errors? And finally, what mechanisms can be envisioned to restore the validity of the scientific record and, if necessary, retract publications that are clearly invalidated by the lack of experimental evidence? We suggest that cognitive bias and flawed epistemology are likely at the root of the problem. By using examples from the published literature and from public repositories such as the Protein Data Bank, we provide case summaries to guide correction or improvement of structural models. When strong claims are unsustainable because of a deficient crystallographic model, removal of such a model and even retraction of the affected publication are necessary to restore the integrity of the scientific record. This article is protected by copyright. All rights reserved. | |
| - | + | Detect, Correct, Retract: How to manage incorrect structural models.,Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B FEBS J. 2017 Nov 7. doi: 10.1111/febs.14320. PMID:29113027<ref>PMID:29113027</ref> | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| Line 24: | Line 25: | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Solanum melongena]] | [[Category: Solanum melongena]] | ||
| - | [[Category: Dauter | + | [[Category: Dauter Z]] |
| - | [[Category: Jaskolski | + | [[Category: Jaskolski M]] |
| - | [[Category: Minor | + | [[Category: Minor W]] |
| - | [[Category: Porebski | + | [[Category: Porebski PJ]] |
| - | [[Category: Pozharski | + | [[Category: Pozharski E]] |
| - | [[Category: Rupp | + | [[Category: Rupp B]] |
| - | [[Category: Stanfield | + | [[Category: Stanfield R]] |
| - | [[Category: Weichenberger | + | [[Category: Weichenberger CX]] |
| - | [[Category: Wlodawer | + | [[Category: Wlodawer A]] |
| - | + | ||
| - | + | ||
Revision as of 13:47, 4 October 2023
Crystal structure of the vicilin from Solanum melongena, re-refinement
| |||||||||||
