2q4h: Difference between revisions
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|PDB= 2q4h |SIZE=350|CAPTION= <scene name='initialview01'>2q4h</scene>, resolution 1.834Å | |PDB= 2q4h |SIZE=350|CAPTION= <scene name='initialview01'>2q4h</scene>, resolution 1.834Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/UDP-glucose--hexose-1-phosphate_uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.12 2.7.7.12] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose--hexose-1-phosphate_uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.12 2.7.7.12] </span> | ||
|GENE= AT5G18200, MRG7_16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana]) | |GENE= AT5G18200, MRG7_16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana]) | ||
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00608 GalT], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG1085 GalT]</span> | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4h OCA], [http://www.ebi.ac.uk/pdbsum/2q4h PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2q4h RCSB]</span> | |||
}} | }} | ||
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[[Category: Levin, E J.]] | [[Category: Levin, E J.]] | ||
[[Category: Wesenberg, G E.]] | [[Category: Wesenberg, G E.]] | ||
[[Category: amp]] | [[Category: amp]] | ||
[[Category: center for eukaryotic structural genomic]] | [[Category: center for eukaryotic structural genomic]] | ||
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[[Category: zinc]] | [[Category: zinc]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:41:44 2008'' | ||
Revision as of 07:41, 26 March 2008
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| , resolution 1.834Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | AT5G18200, MRG7_16 (Arabidopsis thaliana) | ||||||
| Activity: | UDP-glucose--hexose-1-phosphate uridylyltransferase, with EC number 2.7.7.12 | ||||||
| Domains: | GalT, GalT | ||||||
| Resources: | FirstGlance, OCA, PDBsum, JenaLib, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ensemble refinement of the crystal structure of GALT-like protein from Arabidopsis thaliana At5g18200
OverviewOverview
X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.
About this StructureAbout this Structure
2Q4H is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.
ReferenceReference
Ensemble refinement of protein crystal structures: validation and application., Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr, Structure. 2007 Sep;15(9):1040-52. PMID:17850744
Page seeded by OCA on Wed Mar 26 06:41:44 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Arabidopsis thaliana
- Single protein
- UDP-glucose--hexose-1-phosphate uridylyltransferase
- CESG, Center for Eukaryotic Structural Genomics.
- Jr., G N.Phillips.
- Kondrashov, D A.
- Levin, E J.
- Wesenberg, G E.
- Amp
- Center for eukaryotic structural genomic
- Cesg
- Ensemble refinement
- Galt
- Protein structure initiative
- Psi
- Refinement methodology development
- Structural genomic
- Transferase
- Zinc