1xi1: Difference between revisions

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<StructureSection load='1xi1' size='340' side='right'caption='[[1xi1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1xi1' size='340' side='right'caption='[[1xi1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1xi1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XI1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1xi1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XI1 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xhx|1xhx]], [[1xhz|1xhz]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=1xi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xi1 OCA], [https://pdbe.org/1xi1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xi1 RCSB], [https://www.ebi.ac.uk/pdbsum/1xi1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xi1 ProSAT]</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=1xi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xi1 OCA], [https://pdbe.org/1xi1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xi1 RCSB], [https://www.ebi.ac.uk/pdbsum/1xi1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xi1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.  
[https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[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=1xi1 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=1xi1 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In 1954, Howells and colleagues described an unusual diffraction pattern from imidazole methemoglobin crystals caused by lattice-translocation defects. In these crystals, two identical lattices coexist as a single coherent mosaic block, but are translated by a fixed vector with respect to each other. The observed structure is a weighted sum of the two identical but translated structures, one from each lattice; the observed structure factors are a weighted vector sum of the two structure factors with identical unit amplitudes but shifted phases. A general procedure is described to obtain the unit amplitudes of observed structure factors from a realigned single lattice through an X-ray intensity correction. An application of this procedure is made to determine the crystal structure of phi29 DNA polymerase at 2.2 A resolution using multiple isomorphous replacement and multiwavelength anomalous dispersion methods.


Correction of X-ray intensities from single crystals containing lattice-translocation defects.,Wang J, Kamtekar S, Berman AJ, Steitz TA Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):67-74. Epub 2004, Dec 17. PMID:15608377<ref>PMID:15608377</ref>
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1xi1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bpph2]]
[[Category: Bacillus virus phi29]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Berman, A J]]
[[Category: Berman AJ]]
[[Category: Blanco, L]]
[[Category: Blanco L]]
[[Category: Kamtekar, S]]
[[Category: Kamtekar S]]
[[Category: Lazaro, J M]]
[[Category: Lazaro JM]]
[[Category: Salas, M]]
[[Category: Salas M]]
[[Category: Steitz, T A]]
[[Category: Steitz TA]]
[[Category: Vega, M de]]
[[Category: Wang J]]
[[Category: Wang, J]]
[[Category: De Vega M]]
[[Category: Dna polymerase]]
[[Category: Processivity]]
[[Category: Protein-primed]]
[[Category: Replication]]
[[Category: Strand displacement]]
[[Category: Transferase-dna complex]]

Latest revision as of 08:50, 14 February 2024

Phi29 DNA polymerase ssDNA complex, monoclinic crystal form

1xi1, resolution 2.20Å

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