1swz
From Proteopedia
(New page: 200px<br /><applet load="1swz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1swz, resolution 1.06Å" /> '''Use of an ion-bindin...) |
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| - | [[Image:1swz.gif|left|200px]]<br /><applet load="1swz" size=" | + | [[Image:1swz.gif|left|200px]]<br /><applet load="1swz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1swz, resolution 1.06Å" /> | caption="1swz, resolution 1.06Å" /> | ||
'''Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods'''<br /> | '''Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure determination by direct methods'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Proteins with more than 1000 non-H atoms and without heavy-atom prosthetic | + | 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== | ==About this Structure== | ||
| - | 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 PO4, RB, CL and BME 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:// | + | 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]. |
==Reference== | ==Reference== | ||
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[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Matthews, B | + | [[Category: Matthews, B W.]] |
| - | [[Category: Mooers, B | + | [[Category: Mooers, B H.M.]] |
[[Category: BME]] | [[Category: BME]] | ||
[[Category: CL]] | [[Category: CL]] | ||
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[[Category: rb+ binding site]] | [[Category: rb+ binding site]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:06:12 2008'' |
Revision as of 13:06, 21 February 2008
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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 with , , and as ligands. Active as Lysozyme, with EC number 3.2.1.17 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 Thu Feb 21 15:06:12 2008
Categories: Bacteriophage t4 | Lysozyme | Single protein | Matthews, B W. | Mooers, B H.M. | BME | CL | PO4 | RB | Ab initio direct methods | Rb+ binding site
