2q4r: Difference between revisions
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|PDB= 2q4r |SIZE=350|CAPTION= <scene name='initialview01'>2q4r</scene>, resolution 2.090Å | |PDB= 2q4r |SIZE=350|CAPTION= <scene name='initialview01'>2q4r</scene>, resolution 2.090Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> | |LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Phosphomannomutase Phosphomannomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.8 5.4.2.8] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphomannomutase Phosphomannomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.8 5.4.2.8] </span> | ||
|GENE= PMM2, HS.459855 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= PMM2, HS.459855 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03332 PMM]</span> | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4r OCA], [http://www.ebi.ac.uk/pdbsum/2q4r PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2q4r RCSB]</span> | |||
}} | }} | ||
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[[Category: Levin, E J.]] | [[Category: Levin, E J.]] | ||
[[Category: Wesenberg, G E.]] | [[Category: Wesenberg, G E.]] | ||
[[Category: bc008310]] | [[Category: bc008310]] | ||
[[Category: carbohydrate-deficient glycoprotein syndrome]] | [[Category: carbohydrate-deficient glycoprotein syndrome]] | ||
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[[Category: structural genomic]] | [[Category: structural genomic]] | ||
''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 06:42:00 2008'' | ||
Revision as of 07:42, 26 March 2008
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| , resolution 2.090Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | PMM2, HS.459855 (Homo sapiens) | ||||||
| Activity: | Phosphomannomutase, with EC number 5.4.2.8 | ||||||
| Domains: | PMM | ||||||
| Resources: | FirstGlance, OCA, PDBsum, JenaLib, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)
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.
DiseaseDisease
Known disease associated with this structure: Carbohydrate-deficient glycoprotein syndrome, type I OMIM:[601785]
About this StructureAbout this Structure
2Q4R is a Single protein structure of sequence from Homo sapiens. 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 06:42:00 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Homo sapiens
- Phosphomannomutase
- Single protein
- CESG, Center for Eukaryotic Structural Genomics.
- Jr., G N.Phillips.
- Kondrashov, D A.
- Levin, E J.
- Wesenberg, G E.
- Bc008310
- Carbohydrate-deficient glycoprotein syndrome
- Center for eukaryotic structural genomic
- Cesg
- Ensemble refinement
- Had superfamily
- Hs 313504
- Hs 459855
- Isomerase
- Jaecken disease
- Pfam pf03332
- Phosphatase
- Protein structure initiative
- Psi
- Refinement methodology development
- Structural genomic