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1ltm

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Revision as of 08:02, 25 November 2020

ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP

Structural highlights

1ltm is a 1 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	MLTB ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MLTB_ECOLI] Murein-degrading enzyme. Catalyzes the cleavage of the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine residues in peptidoglycan. May play a role in recycling of muropeptides during cell elongation and/or cell division.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The X-ray structure of the 36 kDa soluble lytic transglycosylase from Escherichia coli has been determined starting with the multiple isomorphous replacement method with inclusion of anomalous scattering at 2.7 A resolution. Subsequently, before any model building was carried out, phases were extended to 1.7 A resolution with the weighted automated refinement procedure wARP, which gave a dramatic improvement in the phases. The electron-density maps from wARP were of outstanding quality for both the main chain and the side chains of the protein, which allowed the time spent on the tracing, interpretation and building of the X-ray structure to be substantially shortened. The structure of the soluble lytic transglycosylase was refined at 1.7 A resolution with X-PLOR to a final crystallographic R factor of 18.9%. Analysis of the wARP procedure revealed that the use of the maximum-likelihood refinement in wARP gave much better phases than least-squares refinement, provided that the ratio of reflections to protein atom parameters was approximately 1.8 or higher. Furthermore, setting aside 5% of the data for an Rfree test set had a negative effect on the phase improvement. The mean WwARP, a weight determined at the end of the wARP procedure and based on the variance of structure factors from six individually refined wARP models, proved to be a better indicator than the Rfree factor to judge different phase improvement protocols. The elongated Slt35 structure has three domains named the alpha, beta and core domains. The alpha domain contains mainly alpha-helices, while the beta domain consists of a five-stranded antiparallel beta-sheet flanked by a short alpha-helix. Sandwiched between the alpha and beta domains is the core domain, which bears some resemblance to the fold of the catalytic domain of the previously elucidated 70 kDa soluble lytic transglycosylase from E. coli. The putative active site is at the bottom of a large deep groove in the core domain.

Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP.,Van Asselt EJ, Perrakis A, Kalk KH, Lamzin VS, Dijkstra BW Acta Crystallogr D Biol Crystallogr. 1998 Jan 1;54(Pt 1):58-73. PMID:9761817^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Van Asselt EJ, Perrakis A, Kalk KH, Lamzin VS, Dijkstra BW. Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP. Acta Crystallogr D Biol Crystallogr. 1998 Jan 1;54(Pt 1):58-73. PMID:9761817

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ltm"

@@ Line 1: / Line 1: @@
 ==ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP==
-<StructureSection load='1ltm' size='340' side='right' caption='[[1ltm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='1ltm' size='340' side='right'caption='[[1ltm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ltm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LTM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ltm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LTM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1LTM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MLTB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ltm OCA], [http://pdbe.org/1ltm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ltm RCSB], [http://www.ebi.ac.uk/pdbsum/1ltm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ltm ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ltm OCA], [http://pdbe.org/1ltm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ltm RCSB], [http://www.ebi.ac.uk/pdbsum/1ltm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ltm ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lt/1ltm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lt/1ltm_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: Asselt, E J.Van]]
 [[Category: Dijkstra, B W]]

1ltm

From Proteopedia

Revision as of 08:02, 25 November 2020

ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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