5rnt: Difference between revisions
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< | ==X-RAY ANALYSIS OF CUBIC CRYSTALS OF THE COMPLEX FORMED BETWEEN RIBONUCLEASE T1 AND GUANOSINE-3',5'-BISPHOSPHATE== | ||
<StructureSection load='5rnt' size='340' side='right'caption='[[5rnt]], [[Resolution|resolution]] 3.20Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5rnt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RNT 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]] 3.2Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGP:GUANOSINE-3,5-DIPHOSPHATE'>PGP</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=5rnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rnt OCA], [https://pdbe.org/5rnt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rnt RCSB], [https://www.ebi.ac.uk/pdbsum/5rnt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rnt ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR] | |||
== 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/rn/5rnt_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=5rnt ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The complex formed between ribonuclease T1 (RNase T1) and guanosine-3',5'-bisphosphate (3',5'-pGp) crystallizes in the cubic space group I23 with alpha = 86.47 (4) A. X-ray data were collected on a four-circle diffractometer to 3.2 A resolution and the structure was determined by molecular-replacement methods [ULTIMA; Rabinovich & Shakked (1984). Acta Cryst. A40, 195-200] based on the RNase T1 coordinates taken from the complex with guanosine-2'-phosphate. Refinement converged at 16.6% for 1540 data with Fo greater than 1 sigma (Fo) with acceptable stereochemistry. The RNase T1 conformation is comparable to that in other complexes which crystallize preferentially in space group P2(1)2(1)2(1) except for side chains that interact intermolecularly. The guanine of 3',5'-pGp is bound to the recognition site in the same way as in other guanine-containing complexes except for its interaction with Glu46. The side-chain carboxylate of this amino acid does not form hydrogen bonds to N1H and N2H of guanine but is rotated so as to permit insertion of two water molecules which replace its acceptor functions. In contrast to other guanosine derivatives which are bound to RNase T1 in the syn form, 3',5'-pGp is anti. This conformation positions the two phosphate groups 'outside' the protein, with hydrogen-bonding contacts only to water molecules; the active site is filled by water. The RNase T1-3',5'-pGp complex probably has biological significance as it may represent the enzyme-product complex before dissociation. | |||
X-ray analysis of cubic crystals of the complex formed between ribonuclease T1 and guanosine-3',5'-bisphosphate.,Lenz A, Heinemann U, Maslowska M, Saenger W Acta Crystallogr B. 1991 Aug 1;47 ( Pt 4):521-7. PMID:1930833<ref>PMID:1930833</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5rnt" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Aspergillus oryzae]] | [[Category: Aspergillus oryzae]] | ||
[[Category: Heinemann | [[Category: Large Structures]] | ||
[[Category: Lenz | [[Category: Heinemann U]] | ||
[[Category: Saenger | [[Category: Lenz A]] | ||
[[Category: Saenger W]] | |||
Latest revision as of 07:39, 21 November 2024
X-RAY ANALYSIS OF CUBIC CRYSTALS OF THE COMPLEX FORMED BETWEEN RIBONUCLEASE T1 AND GUANOSINE-3',5'-BISPHOSPHATEX-RAY ANALYSIS OF CUBIC CRYSTALS OF THE COMPLEX FORMED BETWEEN RIBONUCLEASE T1 AND GUANOSINE-3',5'-BISPHOSPHATE
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe complex formed between ribonuclease T1 (RNase T1) and guanosine-3',5'-bisphosphate (3',5'-pGp) crystallizes in the cubic space group I23 with alpha = 86.47 (4) A. X-ray data were collected on a four-circle diffractometer to 3.2 A resolution and the structure was determined by molecular-replacement methods [ULTIMA; Rabinovich & Shakked (1984). Acta Cryst. A40, 195-200] based on the RNase T1 coordinates taken from the complex with guanosine-2'-phosphate. Refinement converged at 16.6% for 1540 data with Fo greater than 1 sigma (Fo) with acceptable stereochemistry. The RNase T1 conformation is comparable to that in other complexes which crystallize preferentially in space group P2(1)2(1)2(1) except for side chains that interact intermolecularly. The guanine of 3',5'-pGp is bound to the recognition site in the same way as in other guanine-containing complexes except for its interaction with Glu46. The side-chain carboxylate of this amino acid does not form hydrogen bonds to N1H and N2H of guanine but is rotated so as to permit insertion of two water molecules which replace its acceptor functions. In contrast to other guanosine derivatives which are bound to RNase T1 in the syn form, 3',5'-pGp is anti. This conformation positions the two phosphate groups 'outside' the protein, with hydrogen-bonding contacts only to water molecules; the active site is filled by water. The RNase T1-3',5'-pGp complex probably has biological significance as it may represent the enzyme-product complex before dissociation. X-ray analysis of cubic crystals of the complex formed between ribonuclease T1 and guanosine-3',5'-bisphosphate.,Lenz A, Heinemann U, Maslowska M, Saenger W Acta Crystallogr B. 1991 Aug 1;47 ( Pt 4):521-7. PMID:1930833[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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