1swz

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[[Image:1swz.gif|left|200px]]<br /><applet load="1swz" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1swz.gif|left|200px]]
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caption="1swz, resolution 1.06&Aring;" />
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'''Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods'''<br />
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{{Structure
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|PDB= 1swz |SIZE=350|CAPTION= <scene name='initialview01'>1swz</scene>, resolution 1.06&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>
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|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]
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|GENE= E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T4])
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}}
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'''Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1SWZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=RB:'>RB</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=BME:'>BME</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SWZ OCA].
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1SWZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SWZ OCA].
==Reference==
==Reference==
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15388918 15388918]
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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: Bacteriophage t4]]
[[Category: Bacteriophage t4]]
[[Category: Lysozyme]]
[[Category: Lysozyme]]
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[[Category: PO4]]
[[Category: PO4]]
[[Category: RB]]
[[Category: RB]]
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[[Category: ab initio direct methods]]
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[[Category: ab initio direct method]]
[[Category: rb+ binding site]]
[[Category: rb+ binding site]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:06:12 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:10:43 2008''

Revision as of 12:10, 20 March 2008

Image:1swz.gif


PDB ID 1swz

Drag the structure with the mouse to rotate
, resolution 1.06Å
Ligands: , , and
Gene: E (Bacteriophage T4)
Activity: Lysozyme, with EC number 3.2.1.17
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 Bacteriophage 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

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