1kj1
From Proteopedia
(New page: 200px<br /><applet load="1kj1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kj1, resolution 2.20Å" /> '''MANNOSE-SPECIFIC AGG...) |
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| - | [[Image:1kj1.gif|left|200px]]<br /><applet load="1kj1" size=" | + | [[Image:1kj1.gif|left|200px]]<br /><applet load="1kj1" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1kj1, resolution 2.20Å" /> | caption="1kj1, resolution 2.20Å" /> | ||
'''MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE'''<br /> | '''MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of dimeric garlic lectin was previously determined to an | + | The structure of dimeric garlic lectin was previously determined to an effective resolution of 2.8A using X-ray intensity data processed by the XDS package and refined using X-PLOR [Chandra et al. (1999), J. Mol. Biol. 285, 1157--1168]. Repeated attempts to grow better crystals with a view to improving the definition of the structure did not succeed. The available raw data were then reprocessed using DENZO. The structure was re-refined with both X-PLOR and CNS separately using the reprocessed data, which extended to a resolution of 2.2A. These two sets of refinements and the two sets using the XDS-processed data afforded an opportunity to compare the performance of different data-processing and refinement packages when dealing with data from weakly diffracting crystals. The best results were obtained when CNS was employed for refinement using data processed by DENZO. The quality and the resolution of the map and the definition of the structure improved substantially. In particular, the amino-acid residues at the variable locations in the sequence, and hence the isolectins, could be identified with a high degree of confidence. It could be established that the crystal asymmetric unit contains two identical heterodimers. The new refined structure also provided a better definition of other finer structural details. |
==About this Structure== | ==About this Structure== | ||
| - | 1KJ1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Allium_sativum Allium sativum] with MAN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1KJ1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Allium_sativum Allium sativum] with <scene name='pdbligand=MAN:'>MAN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KJ1 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Allium sativum]] | [[Category: Allium sativum]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Chandra, N | + | [[Category: Chandra, N R.]] |
[[Category: Ramachandraiah, G.]] | [[Category: Ramachandraiah, G.]] | ||
[[Category: Surolia, A.]] | [[Category: Surolia, A.]] | ||
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[[Category: plant protein]] | [[Category: plant protein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:34:41 2008'' |
Revision as of 11:34, 21 February 2008
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MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE
Overview
The structure of dimeric garlic lectin was previously determined to an effective resolution of 2.8A using X-ray intensity data processed by the XDS package and refined using X-PLOR [Chandra et al. (1999), J. Mol. Biol. 285, 1157--1168]. Repeated attempts to grow better crystals with a view to improving the definition of the structure did not succeed. The available raw data were then reprocessed using DENZO. The structure was re-refined with both X-PLOR and CNS separately using the reprocessed data, which extended to a resolution of 2.2A. These two sets of refinements and the two sets using the XDS-processed data afforded an opportunity to compare the performance of different data-processing and refinement packages when dealing with data from weakly diffracting crystals. The best results were obtained when CNS was employed for refinement using data processed by DENZO. The quality and the resolution of the map and the definition of the structure improved substantially. In particular, the amino-acid residues at the variable locations in the sequence, and hence the isolectins, could be identified with a high degree of confidence. It could be established that the crystal asymmetric unit contains two identical heterodimers. The new refined structure also provided a better definition of other finer structural details.
About this Structure
1KJ1 is a Protein complex structure of sequences from Allium sativum with as ligand. Full crystallographic information is available from OCA.
Reference
Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin., Ramachandraiah G, Chandra NR, Surolia A, Vijayan M, Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):414-20. Epub 2002, Feb 21. PMID:11856826
Page seeded by OCA on Thu Feb 21 13:34:41 2008
