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2blp

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Revision as of 06:13, 16 May 2018

RNase before unattenuated X-RAY burn

Structural highlights

2blp is a 1 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1a2w, 1a5p, 1a5q, 1afk, 1afl, 1afu, 1aqp, 1b6v, 1bel, 1bzq, 1c0b, 1c0c, 1c8w, 1c9v, 1c9x, 1cjq, 1cjr, 1d5d, 1d5e, 1d5h, 1dfj, 1dy5, 1eic, 1eid, 1eie, 1eos, 1eow, 1f0v, 1fev, 1fs3, 1gv7, 1izp, 1izq, 1izr, 1j7z, 1j80, 1j81, 1j82, 1jn4, 1js0, 1jvt, 1jvu, 1jvv, 1kf2, 1kf3, 1kf4, 1kf5, 1kf7, 1kf8, 1kh8, 1lsq, 1o0f, 1o0h, 1o0m, 1o0n, 1o0o, 1qhc, 1rar, 1ras, 1rat, 1rbb, 1rbc, 1rbd, 1rbe, 1rbf, 1rbg, 1rbh, 1rbi, 1rbj, 1rbn, 1rbw, 1rbx, 1rca, 1rcn, 1rha, 1rhb, 1rnc, 1rnd, 1rnm, 1rnn, 1rno, 1rnq, 1rnu, 1rnv, 1rnw, 1rnx, 1rny, 1rnz, 1rob, 1rpf, 1rpg, 1rph, 1rsm, 1rta, 1rtb, 1ruv, 1srn, 1ssa, 1ssb, 1ssc, 1un5, 1w4o, 1w4p, 1w4q, 1wbu, 1xps, 1xpt, 2aas, 2rat, 2rln, 2rns, 3rat, 3rn3, 3rsd, 3rsk, 3rsp, 3srn, 4rat, 4rsd, 4rsk, 4srn, 5rat, 5rsa, 6rat, 6rsa, 7rat, 7rsa, 8rat, 8rsa, 9rat, 9rsa
Activity:	Pancreatic ribonuclease, with EC number 3.1.27.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.^[1]

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

Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.

Improving radiation-damage substructures for RIP.,Nanao MH, Sheldrick GM, Ravelli RB Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37. Epub 2005, Aug 16. PMID:16131756^[2]

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

References

↑ delCardayre SB, Ribo M, Yokel EM, Quirk DJ, Rutter WJ, Raines RT. Engineering ribonuclease A: production, purification and characterization of wild-type enzyme and mutants at Gln11. Protein Eng. 1995 Mar;8(3):261-73. PMID:7479688
↑ Nanao MH, Sheldrick GM, Ravelli RB. Improving radiation-damage substructures for RIP. Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37. Epub 2005, Aug 16. PMID:16131756 doi:10.1107/S0907444905019360

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/2blp"

@@ Line 1: / Line 1: @@
-==RNASE BEFORE UNATTENUATED X-RAY BURN==
+==RNase before unattenuated X-RAY burn==
 <StructureSection load='2blp' size='340' side='right' caption='[[2blp]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1a2w|1a2w]], [[1a5p|1a5p]], [[1a5q|1a5q]], [[1afk|1afk]], [[1afl|1afl]], [[1afu|1afu]], [[1aqp|1aqp]], [[1b6v|1b6v]], [[1bel|1bel]], [[1bzq|1bzq]], [[1c0b|1c0b]], [[1c0c|1c0c]], [[1c8w|1c8w]], [[1c9v|1c9v]], [[1c9x|1c9x]], [[1cjq|1cjq]], [[1cjr|1cjr]], [[1d5d|1d5d]], [[1d5e|1d5e]], [[1d5h|1d5h]], [[1dfj|1dfj]], [[1dy5|1dy5]], [[1eic|1eic]], [[1eid|1eid]], [[1eie|1eie]], [[1eos|1eos]], [[1eow|1eow]], [[1f0v|1f0v]], [[1fev|1fev]], [[1fs3|1fs3]], [[1gv7|1gv7]], [[1izp|1izp]], [[1izq|1izq]], [[1izr|1izr]], [[1j7z|1j7z]], [[1j80|1j80]], [[1j81|1j81]], [[1j82|1j82]], [[1jn4|1jn4]], [[1js0|1js0]], [[1jvt|1jvt]], [[1jvu|1jvu]], [[1jvv|1jvv]], [[1kf2|1kf2]], [[1kf3|1kf3]], [[1kf4|1kf4]], [[1kf5|1kf5]], [[1kf7|1kf7]], [[1kf8|1kf8]], [[1kh8|1kh8]], [[1lsq|1lsq]], [[1o0f|1o0f]], [[1o0h|1o0h]], [[1o0m|1o0m]], [[1o0n|1o0n]], [[1o0o|1o0o]], [[1qhc|1qhc]], [[1rar|1rar]], [[1ras|1ras]], [[1rat|1rat]], [[1rbb|1rbb]], [[1rbc|1rbc]], [[1rbd|1rbd]], [[1rbe|1rbe]], [[1rbf|1rbf]], [[1rbg|1rbg]], [[1rbh|1rbh]], [[1rbi|1rbi]], [[1rbj|1rbj]], [[1rbn|1rbn]], [[1rbw|1rbw]], [[1rbx|1rbx]], [[1rca|1rca]], [[1rcn|1rcn]], [[1rha|1rha]], [[1rhb|1rhb]], [[1rnc|1rnc]], [[1rnd|1rnd]], [[1rnm|1rnm]], [[1rnn|1rnn]], [[1rno|1rno]], [[1rnq|1rnq]], [[1rnu|1rnu]], [[1rnv|1rnv]], [[1rnw|1rnw]], [[1rnx|1rnx]], [[1rny|1rny]], [[1rnz|1rnz]], [[1rob|1rob]], [[1rpf|1rpf]], [[1rpg|1rpg]], [[1rph|1rph]], [[1rsm|1rsm]], [[1rta|1rta]], [[1rtb|1rtb]], [[1ruv|1ruv]], [[1srn|1srn]], [[1ssa|1ssa]], [[1ssb|1ssb]], [[1ssc|1ssc]], [[1un5|1un5]], [[1w4o|1w4o]], [[1w4p|1w4p]], [[1w4q|1w4q]], [[1wbu|1wbu]], [[1xps|1xps]], [[1xpt|1xpt]], [[2aas|2aas]], [[2rat|2rat]], [[2rln|2rln]], [[2rns|2rns]], [[3rat|3rat]], [[3rn3|3rn3]], [[3rsd|3rsd]], [[3rsk|3rsk]], [[3rsp|3rsp]], [[3srn|3srn]], [[4rat|4rat]], [[4rsd|4rsd]], [[4rsk|4rsk]], [[4srn|4srn]], [[5rat|5rat]], [[5rsa|5rsa]], [[6rat|6rat]], [[6rsa|6rsa]], [[7rat|7rat]], [[7rsa|7rsa]], [[8rat|8rat]], [[8rsa|8rsa]], [[9rat|9rat]], [[9rsa|9rsa]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></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=2blp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2blp OCA], [http://pdbe.org/2blp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2blp RCSB], [http://www.ebi.ac.uk/pdbsum/2blp PDBsum]</span></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=2blp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2blp OCA], [http://pdbe.org/2blp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2blp RCSB], [http://www.ebi.ac.uk/pdbsum/2blp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2blp ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/2blp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/2blp_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2blp ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

2blp

From Proteopedia

Revision as of 06:13, 16 May 2018

RNase before unattenuated X-RAY burn

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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