This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1bu3

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

REFINED CRYSTAL STRUCTURE OF CALCIUM-BOUND SILVER HAKE (PI 4.2) PARVALBUMIN AT 1.65 A.

Structural highlights

1bu3 is a 1 chain structure with sequence from Merluccius bilinearis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.65Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PRVB_MERBI In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.

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

Parvalbumins constitute a class of calcium-binding proteins characterized by the presence of several helix-loop-helix (EF-hand) motifs. In a previous study (Revett SP, King G, Shabanowitz J, Hunt DF, Hartman KL, Laue TM, Nelson DJ, 1997, Protein Sci 7:2397-2408), we presented the sequence of the major parvalbumin isoform from the silver hake (Merluccius bilinearis) and presented spectroscopic and structural information on the excised "EF-hand" portion of the protein. In this study, the X-ray crystal structure of the silver hake major parvalbumin has been determined to high resolution, in the frozen state, using the molecular replacement method with the carp parvalbumin structure as a starting model. The crystals are orthorhombic, space group C2221, with a = 75.7 A, b = 80.7 A, and c = 42.1 A. Data were collected from a single crystal grown in 15% glycerol, which served as a cryoprotectant for flash freezing at -188 degrees C. The structure refined to a conventional R-value of 21% (free R 25%) for observed reflections in the range 8 to 1.65 A [1 > 2sigma(I)]. The refined model includes an acetylated amino terminus, 108 residues (characteristic of a beta parvalbumin lineage), 2 calcium ions, and 114 water molecules per protein molecule. The resulting structure was used in molecular dynamics (MD) simulations focused primarily on the dynamics of the ligands coordinating the Ca2+ ions in the CD and EF sites. MD simulations were performed on both the fully Ca2+ loaded protein and on a Ca2+ deficient variant, with Ca2+ only in the CD site. There was substantial agreement between the MD and X-ray results in addressing the issue of mobility of key residues in the calcium-binding sites, especially with regard to the side chain of Ser55 in the CD site and Asp92 in the EF site.

X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B).,Richardson RC, King NM, Harrington DJ, Sun H, Royer WE, Nelson DJ Protein Sci. 2000 Jan;9(1):73-82. PMID:10739249^[1]

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

References

↑ Richardson RC, King NM, Harrington DJ, Sun H, Royer WE, Nelson DJ. X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B). Protein Sci. 2000 Jan;9(1):73-82. PMID:10739249 doi:http://dx.doi.org/10.1110/ps.9.1.73

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/1bu3"

@@ Line 1: / Line 1: @@
 ==REFINED CRYSTAL STRUCTURE OF CALCIUM-BOUND SILVER HAKE (PI 4.2) PARVALBUMIN AT 1.65 A.==
-<StructureSection load='1bu3' size='340' side='right' caption='[[1bu3]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+<StructureSection load='1bu3' size='340' side='right'caption='[[1bu3]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1bu3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Merluccius_bilinearis Merluccius bilinearis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BU3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1bu3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Merluccius_bilinearis Merluccius bilinearis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BU3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.65&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bu3 OCA], [http://pdbe.org/1bu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1bu3 PDBsum]</span></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=1bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bu3 OCA], [https://pdbe.org/1bu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bu3 RCSB], [https://www.ebi.ac.uk/pdbsum/1bu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bu3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PRVB_MERBI PRVB_MERBI]] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.
+[https://www.uniprot.org/uniprot/PRVB_MERBI PRVB_MERBI] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.
 == 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/bu/1bu3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bu/1bu3_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=1bu3 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Merluccius bilinearis]]
-[[Category: Harrington, D J]]
+[[Category: Harrington DJ]]
-[[Category: Nelson, D J]]
+[[Category: Nelson DJ]]
-[[Category: Richardson, R C]]
+[[Category: Richardson RC]]
-[[Category: Royer, W E]]
+[[Category: Royer WE]]
-[[Category: Calcium binding]]

1bu3

From Proteopedia

Current revision

REFINED CRYSTAL STRUCTURE OF CALCIUM-BOUND SILVER HAKE (PI 4.2) PARVALBUMIN AT 1.65 A.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox