1swz
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1swz |SIZE=350|CAPTION= <scene name='initialview01'>1swz</scene>, resolution 1.06Å | |PDB= 1swz |SIZE=350|CAPTION= <scene name='initialview01'>1swz</scene>, resolution 1.06Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</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= E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1swy|1SWY]], [[1sx2|1sx2]], [[1sx7|1sx7]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1swz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1swz OCA], [http://www.ebi.ac.uk/pdbsum/1swz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1swz RCSB]</span> | ||
}} | }} | ||
| Line 16: | Line 19: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1SWZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1SWZ 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=1SWZ OCA]. |
==Reference== | ==Reference== | ||
Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods., Mooers BH, Matthews BW, Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1726-37. Epub 2004, Sep 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15388918 15388918] | Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods., Mooers BH, Matthews BW, Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1726-37. Epub 2004, Sep 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15388918 15388918] | ||
| - | [[Category: | + | [[Category: Enterobacteria phage t4]] |
[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Matthews, B W.]] | [[Category: Matthews, B W.]] | ||
[[Category: Mooers, B H.M.]] | [[Category: Mooers, B H.M.]] | ||
| - | [[Category: BME]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: PO4]] | ||
| - | [[Category: RB]] | ||
[[Category: ab initio direct method]] | [[Category: ab initio direct method]] | ||
[[Category: rb+ binding site]] | [[Category: rb+ binding site]] | ||
| - | ''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 23:48:05 2008'' |
Revision as of 20:48, 30 March 2008
| |||||||
| , resolution 1.06Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | E (Enterobacteria phage T4) | ||||||
| Activity: | Lysozyme, with EC number 3.2.1.17 | ||||||
| Related: | 1SWY, 1sx2, 1sx7
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods
Overview
Proteins with more than 1000 non-H atoms and without heavy-atom prosthetic groups are very difficult to solve by ab initio direct methods. T4 lysozyme is being used to explore these limits. The protein has 1309 non-H atoms, seven S atoms, no disulfide bonds and no heavy-atom prosthetic group. It is recalcitrant to structure determination by direct methods using X-ray diffraction data to 0.97 A. It is shown here that it is possible to obtain a truly ab initio structure determination of a variant of the protein that has an Rb+ (Z = 37) binding site. Using diffraction data to 1.06 A resolution, the direct-methods programs SIR2002 and ACORN independently solved the structure in about 20 h. The bound Rb+, which contributes about 1.7% of the total scattering, does not appear to distort the structure or to inhibit refinement (R factor 12.1%). The phases obtained via SIR2002 or ACORN are in good agreement with those from a reference structure obtained from conventional molecular-substitution and refinement procedures (average error in the figure-of-merit-weighted phases of less than 25 degrees). Thus, proteins with more than 1000 atoms that include halide-binding or other such sites may be amenable to structure determination by ab initio direct methods. The direct-methods approaches are also compared with structure determination via use of the anomalous scattering of the Rb+ ion. As shown by examples, high-resolution structures determined by direct methods can be useful in highlighting regions of strain in the protein, including short hydrogen bonds and non-planar peptide groups.
About this Structure
1SWZ is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods., Mooers BH, Matthews BW, Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1726-37. Epub 2004, Sep 23. PMID:15388918
Page seeded by OCA on Sun Mar 30 23:48:05 2008
