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| | ==Invariom refinement of a new dimeric monoclinic 2 solvate of thiostrepton at 0.64 angstrom resolution== | | ==Invariom refinement of a new dimeric monoclinic 2 solvate of thiostrepton at 0.64 angstrom resolution== |
| - | <StructureSection load='4hp2' size='340' side='right' caption='[[4hp2]], [[Resolution|resolution]] 0.64Å' scene=''> | + | <StructureSection load='4hp2' size='340' side='right'caption='[[4hp2]], [[Resolution|resolution]] 0.64Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4hp2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_azureus Streptomyces azureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HP2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4hp2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_azureus Streptomyces azureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HP2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=ETZ:DIETHYL+ETHER'>ETZ</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]] 0.64Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB9:(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC+ACID'>BB9</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene>, <scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=MH6:3-HYDROXY-2-IMINOPROPANOIC+ACID'>MH6</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=QUA:8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC+ACID'>QUA</scene>, <scene name='pdbligand=TS9:(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC+ACID'>TS9</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB9:(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC+ACID'>BB9</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene>, <scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=ETZ:DIETHYL+ETHER'>ETZ</scene>, <scene name='pdbligand=MH6:3-HYDROXY-2-IMINOPROPANOIC+ACID'>MH6</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=QUA:8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC+ACID'>QUA</scene>, <scene name='pdbligand=TS9:(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC+ACID'>TS9</scene></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=4hp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hp2 OCA], [http://pdbe.org/4hp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hp2 RCSB], [http://www.ebi.ac.uk/pdbsum/4hp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hp2 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=4hp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hp2 OCA], [https://pdbe.org/4hp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hp2 RCSB], [https://www.ebi.ac.uk/pdbsum/4hp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hp2 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/THCL_STRAJ THCL_STRAJ]] Has bacteriocidal activity. Inhibits bacterial protein biosynthesis by acting on the elongation factor Tu (EF-Tu) (By similarity). | + | [https://www.uniprot.org/uniprot/THCL_STRAJ THCL_STRAJ] Has bacteriocidal activity. Inhibits bacterial protein biosynthesis by acting on the elongation factor Tu (EF-Tu) (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Streptomyces azureus]] | | [[Category: Streptomyces azureus]] |
| - | [[Category: Bond, C S]] | + | [[Category: Bond CS]] |
| - | [[Category: Dittrich, B]] | + | [[Category: Dittrich B]] |
| - | [[Category: Holstein, J J]] | + | [[Category: Holstein JJ]] |
| - | [[Category: Huebschle, C B]] | + | [[Category: Huebschle CB]] |
| - | [[Category: Proepper, K]] | + | [[Category: Proepper K]] |
| - | [[Category: Antibacterial]]
| + | |
| - | [[Category: Antibiotic]]
| + | |
| - | [[Category: Oxazole]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Thiazole]]
| + | |
| - | [[Category: Thiazoline]]
| + | |
| - | [[Category: Thiopeptide]]
| + | |
| - | [[Category: Translation inhibition]]
| + | |
| Structural highlights
4hp2 is a 2 chain structure with sequence from Streptomyces azureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 0.64Å |
| Ligands: | , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
THCL_STRAJ Has bacteriocidal activity. Inhibits bacterial protein biosynthesis by acting on the elongation factor Tu (EF-Tu) (By similarity).
Publication Abstract from PubMed
A new monoclinic solvate containing two molecules of the thiopeptide antibiotic thiostrepton in the asymmetric unit has been crystallized in space group P2(1). Single-crystal diffraction data to a resolution of 0.64 A were collected at the SLS synchrotron, allowing structure solution by direct methods and resolution of the disorder present. Valence electron density can be observed in the Fourier residual density from refinement with the independent-atom model, which is a prerequisite for successful application of more sophisticated aspherical-atom scattering factors such as the invariom model when aiming to improve the structural model. Invariom refinement improves quality indicators such as R1(F) for thiostrepton, as previously demonstrated for small molecules. The nonspherical electron-density model also allows the direct derivation of a dipole moment and an electrostatic potential for the whole molecule, which is discussed in the context of antibiotic activity and molecular recognition.
Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64 A resolution.,Propper K, Holstein JJ, Hubschle CB, Bond CS, Dittrich B Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1530-9. doi:, 10.1107/S0907444913010664. Epub 2013 Jul 19. PMID:23897476[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Propper K, Holstein JJ, Hubschle CB, Bond CS, Dittrich B. Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64 A resolution. Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1530-9. doi:, 10.1107/S0907444913010664. Epub 2013 Jul 19. PMID:23897476 doi:10.1107/S0907444913010664
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