1d3m: Difference between revisions
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|PDB= 1d3m |SIZE=350|CAPTION= <scene name='initialview01'>1d3m</scene>, resolution 2.12Å | |PDB= 1d3m |SIZE=350|CAPTION= <scene name='initialview01'>1d3m</scene>, resolution 2.12Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span> | ||
|GENE= GENE E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | |GENE= GENE E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1cx6|1cx6]], [[1cx7|1cx7]], [[1d3m|1D3M]], [[1d3n|1D3N]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3m OCA], [http://www.ebi.ac.uk/pdbsum/1d3m PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d3m RCSB]</span> | |||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
1D3M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | 1D3M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3M OCA]. | ||
==Reference== | ==Reference== | ||
Use of differentially substituted selenomethionine proteins in X-ray structure determination., Gassner NC, Matthews BW, Acta Crystallogr D Biol Crystallogr. 1999 Dec;55(Pt 12):1967-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10666571 10666571] | Use of differentially substituted selenomethionine proteins in X-ray structure determination., Gassner NC, Matthews BW, Acta Crystallogr D Biol Crystallogr. 1999 Dec;55(Pt 12):1967-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10666571 10666571] | ||
[[Category: | [[Category: Enterobacteria phage t4]] | ||
[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Gassner, N C.]] | [[Category: Gassner, N C.]] | ||
[[Category: Matthews, B W.]] | [[Category: Matthews, B W.]] | ||
[[Category: hydrolase (o-glycosyl)]] | [[Category: hydrolase (o-glycosyl)]] | ||
[[Category: methionine core mutant]] | [[Category: methionine core mutant]] | ||
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[[Category: t4 lysozyme]] | [[Category: t4 lysozyme]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:33:59 2008'' | ||
Revision as of 19:34, 30 March 2008
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| , resolution 2.12Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | GENE E (Enterobacteria phage T4) | ||||||
| Activity: | Lysozyme, with EC number 3.2.1.17 | ||||||
| Related: | 1cx6, 1cx7, 1D3M, 1D3N
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
METHIONINE CORE MUTATION
OverviewOverview
Using heavily methionine-substituted T4 lysozyme as an example, it is shown how the addition or deletion of a small number of methionines can simplify the location of selenium sites for use in MAD phasing. By comparing the X-ray data for a large number of singly substituted lysozymes, it is shown that the optimal amino acid to be substituted by methionine is leucine, followed, in order of preference, by phenylalanine, isoleucine and valine. The identification of leucine as the first choice agrees with the ranking suggested by the Dayhoff mutation probability, i.e. by the frequency of amino-acid substitutions in the sequences of related proteins. The ranking of the second and subsequent choices, however, differ significantly.
About this StructureAbout this Structure
1D3M is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
ReferenceReference
Use of differentially substituted selenomethionine proteins in X-ray structure determination., Gassner NC, Matthews BW, Acta Crystallogr D Biol Crystallogr. 1999 Dec;55(Pt 12):1967-70. PMID:10666571
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