ThaumatinV1, Main, Corpus, bibRecord, 000406

Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69 kDa protein.

Identifieur interne : 000406 ( Main/Corpus ); précédent : 000405; suivant : 000407

Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69 kDa protein.

Auteurs : Nobuhisa Watanabe ; Yu Kitago ; Isao Tanaka ; Jia Wei Wang ; Yuan Xin Gu ; Chao De Zheng ; Hai Fu Fan

Source :

Acta crystallographica. Section D, Biological crystallography [ 0907-4449 ] ; 2005.

RBID : pubmed:16239732

English descriptors

KwdEn :
- Aldose-Ketose Isomerases (chemistry), Bacterial Proteins (chemistry), Crystallography, X-Ray (methods), Models, Molecular (MeSH), Muramidase (chemistry), Plant Proteins (chemistry), Proteins (chemistry), Sulfur (chemistry), Trypsin (chemistry).
MESH :
- chemical , chemistry : Aldose-Ketose Isomerases, Bacterial Proteins, Muramidase, Plant Proteins, Proteins, Sulfur, Trypsin.
- methods : Crystallography, X-Ray.
- Models, Molecular.

Abstract

Phasing of the crystal structures of four standard proteins (lysozyme, trypsin, glucose isomerase and thaumatin) and a novel 69 kDa protein from Thermus thermophilus, TT0570, was performed using the single-wavelength anomalous diffraction of S atoms intrinsically present within the native protein molecules. To utilize the sulfur anomalous diffraction, the data sets were collected using the loopless data-collection method with chromium Kalpha X-rays of wavelength 2.29 A. Three phasing methods, MLPHARE, SHARP and OASIS-2004, were tested in combination with the DM or SOLOMON density-modification method. The results showed that the solvent contents are still an important factor for phasing with the S-SAD method, even when longer wavelength Cr Kalpha radiation is used. Of the three procedures, the improved direct phasing of OASIS-2004 with its implemented fragment feedback to the direct-method probability calculation gave the best results in determining the initial phases. For all five proteins, almost the entire models could be built automatically.

DOI: 10.1107/S0907444905028416
PubMed: 16239732

Links to Exploration step

pubmed:16239732

Le document en format XML

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<author><name sortKey="Watanabe, Nobuhisa" sort="Watanabe, Nobuhisa" uniqKey="Watanabe N" first="Nobuhisa" last="Watanabe">Nobuhisa Watanabe</name>
<affiliation><nlm:affiliation>Graduate School of Science, Hokkaido University, Sapporo 0600810, Japan. nobuhisa@sci.hokudai.ac.jp</nlm:affiliation>
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<author><name sortKey="Kitago, Yu" sort="Kitago, Yu" uniqKey="Kitago Y" first="Yu" last="Kitago">Yu Kitago</name>
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<author><name sortKey="Tanaka, Isao" sort="Tanaka, Isao" uniqKey="Tanaka I" first="Isao" last="Tanaka">Isao Tanaka</name>
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<author><name sortKey="Wang, Jia Wei" sort="Wang, Jia Wei" uniqKey="Wang J" first="Jia Wei" last="Wang">Jia Wei Wang</name>
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<author><name sortKey="Gu, Yuan Xin" sort="Gu, Yuan Xin" uniqKey="Gu Y" first="Yuan Xin" last="Gu">Yuan Xin Gu</name>
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<author><name sortKey="Zheng, Chao De" sort="Zheng, Chao De" uniqKey="Zheng C" first="Chao De" last="Zheng">Chao De Zheng</name>
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<author><name sortKey="Fan, Hai Fu" sort="Fan, Hai Fu" uniqKey="Fan H" first="Hai Fu" last="Fan">Hai Fu Fan</name>
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<term>Models, Molecular (MeSH)</term>
<term>Muramidase (chemistry)</term>
<term>Plant Proteins (chemistry)</term>
<term>Proteins (chemistry)</term>
<term>Sulfur (chemistry)</term>
<term>Trypsin (chemistry)</term>
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<front><div type="abstract" xml:lang="en">Phasing of the crystal structures of four standard proteins (lysozyme, trypsin, glucose isomerase and thaumatin) and a novel 69 kDa protein from Thermus thermophilus, TT0570, was performed using the single-wavelength anomalous diffraction of S atoms intrinsically present within the native protein molecules. To utilize the sulfur anomalous diffraction, the data sets were collected using the loopless data-collection method with chromium Kalpha X-rays of wavelength 2.29 A. Three phasing methods, MLPHARE, SHARP and OASIS-2004, were tested in combination with the DM or SOLOMON density-modification method. The results showed that the solvent contents are still an important factor for phasing with the S-SAD method, even when longer wavelength Cr Kalpha radiation is used. Of the three procedures, the improved direct phasing of OASIS-2004 with its implemented fragment feedback to the direct-method probability calculation gave the best results in determining the initial phases. For all five proteins, almost the entire models could be built automatically.</div>
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Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69 kDa protein.

Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69 kDa protein.

Source :

English descriptors

Abstract

Links to Exploration step

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Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

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