2f56

From Proteopedia

(Difference between revisions)

Current revision

Barnase cross-linked with glutaraldehyde soaked in 6M urea

Structural highlights

2f56 is a 3 chain structure with sequence from Bacillus amyloliquefaciens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.955Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNBR_BACAM Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.

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

Structural data about the early step of protein denaturation were obtained from cross-linked crystals for two small proteins: barnase and lysozyme. Several denaturant agents like urea, bromoethanol or thiourea were used at increasing concentrations up to a limit leading to crystal disruption (>or=2 to 6 M). Before the complete destruction of the crystal order started, specific binding sites were observed at the protein surfaces, an indication that the preliminary step of denaturation is the disproportion of intermolecular polar bonds to the benefit of the agent "parasiting" the surface. The analysis of the thermal factors first agree with a stabilization effect at low or moderate concentration of denaturants rapidly followed by a destabilization at specific weak points when the number of sites increase (overflooding effect).

On the edge of the denaturation process: application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations.,Salem M, Mauguen Y, Prange T Biochim Biophys Acta. 2006 May;1764(5):903-12. Epub 2006 Mar 20. PMID:16600702^[1]

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

References

↑ Salem M, Mauguen Y, Prange T. On the edge of the denaturation process: application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations. Biochim Biophys Acta. 2006 May;1764(5):903-12. Epub 2006 Mar 20. PMID:16600702 doi:http://dx.doi.org/10.1016/j.bbapap.2006.02.009

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2f56"

Categories: Bacillus amyloliquefaciens | Large Structures | Prange T | Salem M

@@ Line 3: / Line 3: @@
 <StructureSection load='2f56' size='340' side='right'caption='[[2f56]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2f56]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_amyloliquifaciens"_(sic)_fukumoto_1943 "bacillus amyloliquifaciens" (sic) fukumoto 1943]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F56 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2f56]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F56 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URE:UREA'>URE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.955&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1a2p|1a2p]], [[2f4y|2f4y]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URE:UREA'>URE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2f56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f56 OCA], [https://pdbe.org/2f56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f56 RCSB], [https://www.ebi.ac.uk/pdbsum/2f56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f56 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RNBR_BACAM RNBR_BACAM]] Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.
+[https://www.uniprot.org/uniprot/RNBR_BACAM RNBR_BACAM] Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 37: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus amyloliquefaciens]]
 [[Category: Large Structures]]
-[[Category: Prange, T]]
+[[Category: Prange T]]
-[[Category: Salem, M]]
+[[Category: Salem M]]
-[[Category: Barnase]]
-[[Category: Bromoethanol]]
-[[Category: Cross-linked crystal]]
-[[Category: Denaturation]]
-[[Category: Glutaraldehyde]]
-[[Category: Hydrolase]]
-[[Category: Lysozyme]]
-[[Category: Thiourea]]
-[[Category: Urea]]

2f56

From Proteopedia

Current revision

Barnase cross-linked with glutaraldehyde soaked in 6M urea

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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