Asymmetric Unit: Difference between revisions
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* <scene name='Asymmetric_Unit/Asymmetric_unit/1'>Asymmetric Unit</scene>. | * <scene name='Asymmetric_Unit/Asymmetric_unit/1'>Asymmetric Unit</scene>. | ||
* <scene name='Asymmetric_Unit/Biological_unit/1'>Biological Unit</scene> (obtained from the [http://pqs.ebi.ac.uk Probable Quaternary Structure server at the European Bioinformatics Institute]). In the case of [[2qcb]], it is a homotetramer of the asymmetric unit. | * <scene name='Asymmetric_Unit/Biological_unit/1'>Biological Unit</scene> (obtained from the [http://pqs.ebi.ac.uk Probable Quaternary Structure server at the European Bioinformatics Institute]). In the case of [[2qcb]], it is a homotetramer of the asymmetric unit. | ||
* <scene name='Asymmetric_Unit/Unit_cell/5'>Unit Cell</scene>. In the case of [[2qcb]], the unit cell contains portions of 16 copies of the asymmetric unit. <font color="red">Sorry, still not working. See instructions below.</font> | * <scene name='Asymmetric_Unit/Unit_cell/5'>Unit Cell</scene>. In the case of [[2qcb]], the unit cell contains portions of 16 copies of the asymmetric unit. <!--<font color="red">Sorry, still not working. See instructions below.</font>--> | ||
The '''asymmetric unit''' is the smallest portion of a crystal that | The '''asymmetric unit''' is the smallest portion of a crystal that provides a complete solution. When duplicated and moved by crystal symmetry operations, the unit cell of the crystal can be generated, and from the unit cell, large portions of the crystal. The symmetry operations that are common for biological molecules are rotation, translation, and screw operations (which combine rotation and translation). Mirror symmetry planes occur rarely in crystals of biological molecules due to the presence of chiral centers, e.g. L or D amino acids. | ||
The '''[[Biological Unit|biological unit]]''' is defined elsewhere. | The '''[[Biological Unit|biological unit]]''' is defined elsewhere. | ||
The '''unit cell''' is the smallest portion of a crystal that, when duplicated and translated, can generate the entire crystal. | The '''unit cell''' is the smallest portion of a crystal that, when duplicated and translated, can generate the entire crystal. | ||
<blockquote> | |||
<font color="gray">If the green link "Unit Cell" above is not working, you can '''see the unit cell''' by right-clicking on the molecule in JSmol, and then on the menu that appears, | |||
<!--Style, Unit Cell, On. You can populate the unit cell from Jmol's menu with --> | |||
Symmetry, Reload {1 1 1}.</font> | |||
</blockquote> | |||
==Websites== | ==Websites== | ||
*Diagrams illustrating these concepts are available at the [ | *Diagrams illustrating these concepts are available at the [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies RCSB Protein Data Bank]. | ||
*[http://www.usm.maine.edu/~rhodes/ModQual/ Glossary of Terms from Crystallography, NMR, and Homology Modeling] | *[http://www.usm.maine.edu/~rhodes/ModQual/ Glossary of Terms from Crystallography, NMR, and Homology Modeling] | ||
*[http://reference.iucr.org/dictionary/Asymmetric_unit Asymmetric unit] at the [http://reference.iucr.org/dictionary/Main_Page Online Dictionary of Crystallography] of the International Union of Crystallographers. | *[http://reference.iucr.org/dictionary/Asymmetric_unit Asymmetric unit] at the [http://reference.iucr.org/dictionary/Main_Page Online Dictionary of Crystallography] of the International Union of Crystallographers. | ||
Latest revision as of 19:50, 4 September 2023
The asymmetric unit (see definition below) is what is contained in the model that crystallographers publish in the Protein Data Bank. It is not to be confused with the biologically functional unit (Biological Unit), which may be the same, smaller, or larger than the asymmetric unit.
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Show the:
- .
- (obtained from the Probable Quaternary Structure server at the European Bioinformatics Institute). In the case of 2qcb, it is a homotetramer of the asymmetric unit.
- . In the case of 2qcb, the unit cell contains portions of 16 copies of the asymmetric unit.
The asymmetric unit is the smallest portion of a crystal that provides a complete solution. When duplicated and moved by crystal symmetry operations, the unit cell of the crystal can be generated, and from the unit cell, large portions of the crystal. The symmetry operations that are common for biological molecules are rotation, translation, and screw operations (which combine rotation and translation). Mirror symmetry planes occur rarely in crystals of biological molecules due to the presence of chiral centers, e.g. L or D amino acids.
The biological unit is defined elsewhere.
The unit cell is the smallest portion of a crystal that, when duplicated and translated, can generate the entire crystal.
If the green link "Unit Cell" above is not working, you can see the unit cell by right-clicking on the molecule in JSmol, and then on the menu that appears, Symmetry, Reload {1 1 1}.
WebsitesWebsites
- Diagrams illustrating these concepts are available at the RCSB Protein Data Bank.
- Asymmetric unit at the Online Dictionary of Crystallography of the International Union of Crystallographers.