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3urp

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==Re-refinement of PDB entry 5RNT - ribonuclease T1 with guanosine-3',5'-diphosphate and phosphate ion bound==
==Re-refinement of PDB entry 5RNT - ribonuclease T1 with guanosine-3',5'-diphosphate and phosphate ion bound==
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<StructureSection load='3urp' size='340' side='right' caption='[[3urp]], [[Resolution|resolution]] 3.19&Aring;' scene=''>
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<StructureSection load='3urp' size='340' side='right'caption='[[3urp]], [[Resolution|resolution]] 3.19&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3urp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3URP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3URP FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3urp]] 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=3URP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3URP FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGP:GUANOSINE-3,5-DIPHOSPHATE'>PGP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.19&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5rnt|5rnt]]</td></tr>
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<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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3urp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3urp OCA], [https://pdbe.org/3urp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3urp RCSB], [https://www.ebi.ac.uk/pdbsum/3urp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3urp ProSAT]</span></td></tr>
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<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=3urp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3urp OCA], [http://pdbe.org/3urp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3urp RCSB], [http://www.ebi.ac.uk/pdbsum/3urp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3urp ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR]
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The ternary complex formed between RNase T1, guanosine 3',5'-bisphosphate (3',5'-pGp) and Pi crystallizes in the cubic space group I23 with a = 8.706(1) nm. In a previous publication [Lenz, A., Heinemann, U., Maslowska, M. &amp; Saenger, W. (1991) Acta Crystallogr. B47, 521-527], the structure of the complex (in which Pi was not located) was described at a resolution of 0.32 nm. This is now extended to 0.19 nm with newly grown, larger crystals. Refinement with restrained least-squares converged at R = 17.8% for 8027 reflections with [Fo[ &gt; or = 1 sigma ([Fo[); the final model comprises 120 water molecules. 3',5'-pGp is bound to RNase T1 in the anti form, with guanine in the specific recognition site; the 3'-phosphate protrudes into the solvent, and the 5'-phosphate hydrogen bonds with Lys41 O and Asn43 N4. A tetrahedral anion assigned as Pi occupies the catalytic site and hydrogen bonds to the side chains of Tyr38, Glu58, Arg77 and His92. The overall polypeptide fold of RNase T1 in the cubic space group does not differ significantly from that in the orthorhombic space group P2(1)2(1)2(1) except for changes &lt; or = 0.2 nm in loop regions 69-72 and 95-98.
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Three-dimensional structure of the ternary complex between ribonuclease T1, guanosine 3',5'-bisphosphate and inorganic phosphate at 0.19 nm resolution.,Lenz A, Choe HW, Granzin J, Heinemann U, Saenger W Eur J Biochem. 1993 Jan 15;211(1-2):311-6. PMID:8425541<ref>PMID:8425541</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3urp" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Ribonuclease|Ribonuclease]]
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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*[[Temp|Temp]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
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[[Category: Bricogne, G]]
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[[Category: Large Structures]]
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[[Category: Flensburg, C]]
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[[Category: Bricogne G]]
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[[Category: Keller, P]]
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[[Category: Flensburg C]]
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[[Category: Paciorek, W]]
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[[Category: Keller P]]
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[[Category: Sharff, A]]
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[[Category: Paciorek W]]
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[[Category: Smart, O S]]
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[[Category: Sharff A]]
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[[Category: Vonrhein, C]]
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[[Category: Smart OS]]
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[[Category: Womack, T O]]
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[[Category: Vonrhein C]]
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[[Category: Endoribonuclease]]
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[[Category: Womack TO]]
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[[Category: Hydrolase]]
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[[Category: Rna]]
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[[Category: Roll]]
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Current revision

Re-refinement of PDB entry 5RNT - ribonuclease T1 with guanosine-3',5'-diphosphate and phosphate ion bound

PDB ID 3urp

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