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.


1i6k

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1i6k" size="450" color="white" frame="true" align="right" spinBox="true" caption="1i6k, resolution 1.72&Aring;" /> '''1.7 HIGH RESOLUTION ...)
Current revision (07:44, 3 April 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1i6k.jpg|left|200px]]<br /><applet load="1i6k" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1i6k, resolution 1.72&Aring;" />
 
-
'''1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP'''<br />
 
-
==Overview==
+
==1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP==
-
Native data, anomalous data at three wavelengths and an independent, peak-wavelength data set for SeMet-substituted protein have been collected, from cryoprotected crystals of the TrpRS-adenylate product (TAM) complex, to a resolution limit of 1.7 A. Independent phase sets were developed, using SHARP and improved by solvent flipping with SOLOMON using molecular, envelopes derived from experimental densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their, M(S)IRAS combinations with native data. Hendrickson-Lattman, phase-probability coefficients from each phase set were used in BUSTER to, drive maximum-likelihood refinements of well defined parts of the, previously refined room-temperature 2.9 A structure. Maximum-entropy, completion followed by manual rebuilding was then used to generate a model, for the missing segments, bound ligand and solvent molecules., Surprisingly, peak-wavelength SAD experiments produced the smallest phase, errors relative to the refined structures. Selenomethionylated models, deviate from one another by 0.25 A and from the native model by 0.38 A, but all have r.m.s. deviations of approximately 1.0 A from the 2.9 A, model. Difference Fourier calculations between amplitudes from the 300 K, experiment and the new amplitudes at 100 K using 1.7 A model phases show, no significant structural changes arising from temperature variation or, addition of cryoprotectant. The main differences between low- and, high-resolution structures arise from correcting side-chain rotamers in, the core of the protein as well as on the surface. These changes improve, various structure-validation criteria.
+
<StructureSection load='1i6k' size='340' side='right'caption='[[1i6k]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1i6k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I6K 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]] 1.72&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYM:TRYPTOPHANYL-5AMP'>TYM</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=1i6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i6k OCA], [https://pdbe.org/1i6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i6k RCSB], [https://www.ebi.ac.uk/pdbsum/1i6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i6k ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SYW_GEOSE SYW_GEOSE]
 +
== 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/i6/1i6k_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=1i6k ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1I6K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with SO4, NH4, TYM and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1I6K OCA].
+
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5'AMP., Retailleau P, Yin Y, Hu M, Roach J, Bricogne G, Vonrhein C, Roversi P, Blanc E, Sweet RM, Carter CW Jr, Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1595-608. Epub, 2001 Oct 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11679724 11679724]
+
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Tryptophan--tRNA ligase]]
+
[[Category: Carter CW]]
-
[[Category: Carter, C.W.]]
+
[[Category: Retailleau P]]
-
[[Category: Retailleau, P.]]
+
-
[[Category: GOL]]
+
-
[[Category: NH4]]
+
-
[[Category: SO4]]
+
-
[[Category: TYM]]
+
-
[[Category: aars]]
+
-
[[Category: class i trna synthetase]]
+
-
[[Category: induced fit]]
+
-
[[Category: trprs]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:05:51 2007''
+

Current revision

1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP

PDB ID 1i6k

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/1i6k"
Personal tools