1pnc: Difference between revisions

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 <StructureSection load='1pnc' size='340' side='right'caption='[[1pnc]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pnc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lombardy_poplar Lombardy poplar]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PNC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pnc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Populus_nigra Populus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PNC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=1pnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pnc OCA], [https://pdbe.org/1pnc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pnc RCSB], [https://www.ebi.ac.uk/pdbsum/1pnc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pnc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PLAS1_POPNI PLAS1_POPNI]] Participates in electron transfer between P700 and the cytochrome b6-f complex in photosystem I.
+[https://www.uniprot.org/uniprot/PLAS1_POPNI PLAS1_POPNI] Participates in electron transfer between P700 and the cytochrome b6-f complex in photosystem I.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1pnc ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structure of the copper protein plastocyanin from poplar leaves (Populus nigra var. italica) at 173 K has been subjected to two independent refinements, using a single set of synchrotron X-ray data at 1.6 A resolution. Energy-restrained refinement using the program EREF resulted in lower root-mean-square deviations from ideal geometry (e.g. 0.011 A for bond lengths) but a higher residual R (0.153) than restrained least-squares refinement using the program PROLSQ (0.014 A, 0.132). Electron-density difference maps in both refinements provided evidence for disorder at some side chains and solvent atoms, and the PROLSQ refinement made allowance for this disorder. The number of solvent sites identified at the 4sigma(rho) level was 171 in the EREF refinement and 189 in the PROLSQ refinement; 159 of the solvent sites are common to both refinements within 1 A. The root-mean-square differences between the atomic positions produced by the two refinements are 0.08 A for C(alpha) atoms, 0.08 A for backbone atoms and 0.12 A for all non-H atoms (excluding six obvious outliers) of the protein molecule. The two sets of Cu-ligand bond lengths differ by up to 0.07 A, and the ligand-Cu-ligand angles by up to 7 degrees. At 173 K the volume of the unit cell is 4.2% smaller than at 295 K. Greater order in the solvent region is indicated by the location of 79 more solvent sites, the identification of extensive networks of hydrogen-bonded rings of solvent molecules, and a general decrease in the thermal parameters. Within the unit cell, the protein molecules are significantly translated and rotated from their positions at ambient temperature. An important structural change at low temperature is a 180 degrees flip of the peptide group at Ser48-Gly49. Nearly all other significant differences between the structures of the protein at 173 and 295 K occur at exposed side chains. If the backbone atoms in the 173 and 295 K structures are superposed, excluding atoms involved in the peptide flip, the root-mean- square difference between the positions of 393 atoms is 0.25 A. Two internal water molecules, not included in previous descriptions of poplar plastocyanin, have been located. The plastocyanin Cu-site geometry at 173 K is not significantly different from that at 295 K. If plastocyanin undergoes a change in Cu-site geometry at low temperature, as has been suggested on the basis of resonance Raman spectroscopic evidence, then the change is not detected within the limits of precision of the present results.
-Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K.,Fields BA, Bartsch HH, Bartunik HD, Cordes F, Guss JM, Freeman HC Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):709-30. PMID:15299368<ref>PMID:15299368</ref>
+==See Also==
+*[[Plastocyanin 3D structures|Plastocyanin 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1pnc" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lombardy poplar]]
+[[Category: Populus nigra]]
-[[Category: Fields, B A]]
+[[Category: Fields BA]]
-[[Category: Freeman, H C]]
+[[Category: Freeman HC]]
-[[Category: Guss, J M]]
+[[Category: Guss JM]]
-[[Category: Electron transport]]