This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1tec

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:39, 14 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1tec.jpg|left|200px]]
 
-
{{Structure
+
==CRYSTALLOGRAPHIC REFINEMENT BY INCORPORATION OF MOLECULAR DYNAMICS. THE THERMOSTABLE SERINE PROTEASE THERMITASE COMPLEXED WITH EGLIN-C==
-
|PDB= 1tec |SIZE=350|CAPTION= <scene name='initialview01'>1tec</scene>, resolution 2.2&Aring;
+
<StructureSection load='1tec' size='340' side='right'caption='[[1tec]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
+
<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>
-
|ACTIVITY= [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]
+
</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>
-
|GENE=
+
<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>
-
'''CRYSTALLOGRAPHIC REFINEMENT BY INCORPORATION OF MOLECULAR DYNAMICS. THE THERMOSTABLE SERINE PROTEASE THERMITASE COMPLEXED WITH EGLIN-C'''
+
==See Also==
-
 
+
*[[Eglin|Eglin]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
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.
+
-
 
+
-
==About this Structure==
+
-
1TEC is a [[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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TEC OCA].
+
-
 
+
-
==Reference==
+
-
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://www.ncbi.nlm.nih.gov/pubmed/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 Mar 20 14:17:15 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