1hj9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:20, 9 April 2025) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1hj9.jpg|left|200px]]
 
-
{{Structure
+
==Atomic resolution structures of trypsin provide insight into structural radiation damage==
-
|PDB= 1hj9 |SIZE=350|CAPTION= <scene name='initialview01'>1hj9</scene>, resolution 0.95&Aring;
+
<StructureSection load='1hj9' size='340' side='right'caption='[[1hj9]], [[Resolution|resolution]] 0.95&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=ANL:Ca+Binding+Site+For+Residue+A1001'>ANL</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=ANL:ANILINE'>ANL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+
<table><tr><td colspan='2'>[[1hj9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HJ9 FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.95&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANL:ANILINE'>ANL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hj9 OCA], [https://pdbe.org/1hj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hj9 RCSB], [https://www.ebi.ac.uk/pdbsum/1hj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hj9 ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1hj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hj9 OCA], [http://www.ebi.ac.uk/pdbsum/1hj9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1hj9 RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
 +
== 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/hj/1hj9_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=1hj9 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Radiation damage is an inherent problem in protein X-ray crystallography and the process has recently been shown to be highly specific, exhibiting features such as cleavage of disulfide bonds, decarboxylation of acidic residues, increase in atomic B factors and increase in unit-cell volume. Reported here are two trypsin structures at atomic resolution (1.00 and 0.95 A), the data for which were collected at a third-generation synchrotron (ESRF) at two different beamlines. Both trypsin structures exhibit broken disulfide bonds; in particular, the bond from Cys191 to Cys220 is very sensitive to synchrotron radiation. The data set collected at the most intense beamline (ID14-EH4) shows increased structural radiation damage in terms of lower occupancies for cysteine residues, more breakage in the six disulfide bonds and more alternate conformations. It appears that high intensity and not only the total X-ray dose is most harmful to protein crystals.
-
'''ATOMIC RESOLUTION STRUCTURES OF TRYPSIN PROVIDE INSIGHT INTO STRUCTURAL RADIATION DAMAGE'''
+
Atomic resolution structures of trypsin provide insight into structural radiation damage.,Leiros HK, McSweeney SM, Smalas AO Acta Crystallogr D Biol Crystallogr. 2001 Apr;57(Pt 4):488-97. PMID:11264577<ref>PMID:11264577</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1hj9" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
Radiation damage is an inherent problem in protein X-ray crystallography and the process has recently been shown to be highly specific, exhibiting features such as cleavage of disulfide bonds, decarboxylation of acidic residues, increase in atomic B factors and increase in unit-cell volume. Reported here are two trypsin structures at atomic resolution (1.00 and 0.95 A), the data for which were collected at a third-generation synchrotron (ESRF) at two different beamlines. Both trypsin structures exhibit broken disulfide bonds; in particular, the bond from Cys191 to Cys220 is very sensitive to synchrotron radiation. The data set collected at the most intense beamline (ID14-EH4) shows increased structural radiation damage in terms of lower occupancies for cysteine residues, more breakage in the six disulfide bonds and more alternate conformations. It appears that high intensity and not only the total X-ray dose is most harmful to protein crystals.
+
*[[Trypsin 3D structures|Trypsin 3D structures]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1HJ9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HJ9 OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
-
Atomic resolution structures of trypsin provide insight into structural radiation damage., Leiros HK, McSweeney SM, Smalas AO, Acta Crystallogr D Biol Crystallogr. 2001 Apr;57(Pt 4):488-97. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11264577 11264577]
+
[[Category: Bos taurus]]
[[Category: Bos taurus]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Trypsin]]
+
[[Category: Leiros H-KS]]
-
[[Category: Leiros, H K.S.]]
+
[[Category: McSweeney SM]]
-
[[Category: Mcsweeney, S M.]]
+
[[Category: Smalas AO]]
-
[[Category: Smalas, A O.]]
+
-
[[Category: atomic resolution]]
+
-
[[Category: disulphid bond breakage]]
+
-
[[Category: radiation damage]]
+
-
[[Category: serine proteinase]]
+
-
[[Category: trypsin]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:06:03 2008''
+

Current revision

Atomic resolution structures of trypsin provide insight into structural radiation damage

PDB ID 1hj9

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1hj9"
Personal tools