1tec

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:39, 14 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1tec.jpg|left|200px]]<br /><applet load="1tec" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1tec, resolution 2.2&Aring;" />
 
-
'''CRYSTALLOGRAPHIC REFINEMENT BY INCORPORATION OF MOLECULAR DYNAMICS. THE THERMOSTABLE SERINE PROTEASE THERMITASE COMPLEXED WITH EGLIN-C'''<br />
 
-
==Overview==
+
==CRYSTALLOGRAPHIC REFINEMENT BY INCORPORATION OF MOLECULAR DYNAMICS. THE THERMOSTABLE SERINE PROTEASE THERMITASE COMPLEXED WITH EGLIN-C==
-
In order to investigate the principles of protein thermostability, the crystal structure of thermitase from Thermoactinomyces vulgaris, a thermostable member of the subtilisin family of serine proteases, has been determined in a complex with eglin c. Eglin c is a serine protease inhibitor from the leech Hirudo medicinalis. After data collection with a television area-detector diffractometer and initial structure solution by molecular-replacement methods, crystallographic refinement proceeded with incorporation of molecular-dynamics techniques. It appeared that this refinement procedure has a large convergence radius with movements of more than 5 A for many atoms. Two procedures for the crystallographic molecular-dynamics refinement have been tested. They differed mainly in time span and weight on the X-ray 'energy'. The best results were obtained with a procedure which allowed the molecular-dynamics technique to search a large area in conformational space by having less weight on the X-ray restraints and allowing more time. The use of molecular-dynamics refinement considerably simplified the laborious and difficult task of fitting the model in its electron density during the refinement process. The final crystallographic R factor is 17.9% at 2.2 A resolution.
+
<StructureSection load='1tec' size='340' side='right'caption='[[1tec]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1tec]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hirudo_medicinalis Hirudo medicinalis] and [https://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TEC FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1tec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tec OCA], [https://pdbe.org/1tec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tec RCSB], [https://www.ebi.ac.uk/pdbsum/1tec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tec ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/THET_THEVU THET_THEVU]
 +
== 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/te/1tec_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=1tec ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1TEC is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Hirudo_medicinalis Hirudo medicinalis] and [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Thermitase Thermitase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.66 3.4.21.66] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TEC OCA].
+
*[[Eglin|Eglin]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystallographic refinement by incorporation of molecular dynamics: thermostable serine protease thermitase complexed with eglin c., Gros P, Fujinaga M, Dijkstra BW, Kalk KH, Hol WG, Acta Crystallogr B. 1989 Oct 1;45 ( Pt 5):488-99. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2688688 2688688]
+
[[Category: Hirudo medicinalis]]
[[Category: Hirudo medicinalis]]
-
[[Category: Protein complex]]
+
[[Category: Large Structures]]
-
[[Category: Thermitase]]
+
[[Category: Thermoactinomyces vulgaris]]
[[Category: Thermoactinomyces vulgaris]]
-
[[Category: Dijkstra, B W.]]
+
[[Category: Dijkstra BW]]
-
[[Category: Gros, P.]]
+
[[Category: Gros P]]
-
[[Category: Hol, W G.J.]]
+
[[Category: Hol WGJ]]
-
[[Category: CA]]
+
-
[[Category: NA]]
+
-
[[Category: complex(serine proteinase-inhibitor)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:12:39 2008''
+

Current revision

CRYSTALLOGRAPHIC REFINEMENT BY INCORPORATION OF MOLECULAR DYNAMICS. THE THERMOSTABLE SERINE PROTEASE THERMITASE COMPLEXED WITH EGLIN-C

PDB ID 1tec

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1tec"
Personal tools