Improving radiation-damage substructures for RIP.
Identifieur interne : 000409 ( Main/Exploration ); précédent : 000408; suivant : 000410Improving radiation-damage substructures for RIP.
Auteurs : Max H. Nanao [France] ; George M. Sheldrick ; Raimond B G. RavelliSource :
- Acta crystallographica. Section D, Biological crystallography [ 0907-4449 ] ; 2005.
Descripteurs français
- KwdFr :
- Animaux (MeSH), Disulfures (composition chimique), Disulfures (effets des radiations), Effets des rayonnements (MeSH), Enzymes (composition chimique), Enzymes (effets des radiations), Insuline (composition chimique), Insuline (effets des radiations), Lysozyme (composition chimique), Lysozyme (effets des radiations), Méthodes (MeSH), Pancreatic elastase (composition chimique), Pancreatic elastase (effets des radiations), Pancreatic ribonuclease (composition chimique), Pancreatic ribonuclease (effets des radiations), Protéines végétales (composition chimique), Protéines végétales (effets des radiations), Structure moléculaire (MeSH), Synchrotrons (MeSH), Trypsine (composition chimique), Trypsine (effets des radiations).
- MESH :
- composition chimique : Disulfures, Enzymes, Insuline, Lysozyme, Pancreatic elastase, Pancreatic ribonuclease, Protéines végétales, Trypsine.
- effets des radiations : Disulfures, Enzymes, Insuline, Lysozyme, Pancreatic elastase, Pancreatic ribonuclease, Protéines végétales, Trypsine.
- Animaux, Effets des rayonnements, Méthodes, Structure moléculaire, Synchrotrons.
English descriptors
- KwdEn :
- Animals (MeSH), Disulfides (chemistry), Disulfides (radiation effects), Enzymes (chemistry), Enzymes (radiation effects), Insulin (chemistry), Insulin (radiation effects), Methods (MeSH), Molecular Structure (MeSH), Muramidase (chemistry), Muramidase (radiation effects), Pancreatic Elastase (chemistry), Pancreatic Elastase (radiation effects), Plant Proteins (chemistry), Plant Proteins (radiation effects), Radiation Effects (MeSH), Ribonuclease, Pancreatic (chemistry), Ribonuclease, Pancreatic (radiation effects), Synchrotrons (MeSH), Trypsin (chemistry), Trypsin (radiation effects).
- MESH :
- chemical , chemistry : Disulfides, Enzymes, Insulin, Muramidase, Pancreatic Elastase, Plant Proteins, Ribonuclease, Pancreatic, Trypsin.
- chemical , radiation effects : Disulfides, Enzymes, Insulin, Muramidase, Pancreatic Elastase, Plant Proteins, Ribonuclease, Pancreatic, Trypsin.
- Animals, Methods, Molecular Structure, Radiation Effects, Synchrotrons.
Abstract
Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.
DOI: 10.1107/S0907444905019360
PubMed: 16131756
Affiliations:
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Nanao</name><affiliation wicri:level="3"><nlm:affiliation>EMBL, 6 Rue Jules Horowitz, 38042 Grenoble, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>EMBL, 6 Rue Jules Horowitz, 38042 Grenoble</wicri:regionArea><placeName><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Sheldrick, George M" sort="Sheldrick, George M" uniqKey="Sheldrick G" first="George M" last="Sheldrick">George M. Sheldrick</name></author><author><name sortKey="Ravelli, Raimond B G" sort="Ravelli, Raimond B G" uniqKey="Ravelli R" first="Raimond B G" last="Ravelli">Raimond B G. Ravelli</name></author></analytic><series><title level="j">Acta crystallographica. Section D, Biological crystallography</title><idno type="ISSN">0907-4449</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals (MeSH)</term><term>Disulfides (chemistry)</term><term>Disulfides (radiation effects)</term><term>Enzymes (chemistry)</term><term>Enzymes (radiation effects)</term><term>Insulin (chemistry)</term><term>Insulin (radiation effects)</term><term>Methods (MeSH)</term><term>Molecular Structure (MeSH)</term><term>Muramidase (chemistry)</term><term>Muramidase (radiation effects)</term><term>Pancreatic Elastase (chemistry)</term><term>Pancreatic Elastase (radiation effects)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (radiation effects)</term><term>Radiation Effects (MeSH)</term><term>Ribonuclease, Pancreatic (chemistry)</term><term>Ribonuclease, Pancreatic (radiation effects)</term><term>Synchrotrons (MeSH)</term><term>Trypsin (chemistry)</term><term>Trypsin (radiation effects)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux (MeSH)</term><term>Disulfures (composition chimique)</term><term>Disulfures (effets des radiations)</term><term>Effets des rayonnements (MeSH)</term><term>Enzymes (composition chimique)</term><term>Enzymes (effets des radiations)</term><term>Insuline (composition chimique)</term><term>Insuline (effets des radiations)</term><term>Lysozyme (composition chimique)</term><term>Lysozyme (effets des radiations)</term><term>Méthodes (MeSH)</term><term>Pancreatic elastase (composition chimique)</term><term>Pancreatic elastase (effets des radiations)</term><term>Pancreatic ribonuclease (composition chimique)</term><term>Pancreatic ribonuclease (effets des radiations)</term><term>Protéines végétales (composition chimique)</term><term>Protéines végétales (effets des radiations)</term><term>Structure moléculaire (MeSH)</term><term>Synchrotrons (MeSH)</term><term>Trypsine (composition chimique)</term><term>Trypsine (effets des radiations)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Disulfides</term><term>Enzymes</term><term>Insulin</term><term>Muramidase</term><term>Pancreatic Elastase</term><term>Plant Proteins</term><term>Ribonuclease, Pancreatic</term><term>Trypsin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="radiation effects" xml:lang="en"><term>Disulfides</term><term>Enzymes</term><term>Insulin</term><term>Muramidase</term><term>Pancreatic Elastase</term><term>Plant Proteins</term><term>Ribonuclease, Pancreatic</term><term>Trypsin</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Disulfures</term><term>Enzymes</term><term>Insuline</term><term>Lysozyme</term><term>Pancreatic elastase</term><term>Pancreatic ribonuclease</term><term>Protéines végétales</term><term>Trypsine</term></keywords><keywords scheme="MESH" qualifier="effets des radiations" xml:lang="fr"><term>Disulfures</term><term>Enzymes</term><term>Insuline</term><term>Lysozyme</term><term>Pancreatic elastase</term><term>Pancreatic ribonuclease</term><term>Protéines végétales</term><term>Trypsine</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Methods</term><term>Molecular Structure</term><term>Radiation Effects</term><term>Synchrotrons</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Effets des rayonnements</term><term>Méthodes</term><term>Structure moléculaire</term><term>Synchrotrons</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16131756</PMID><DateCompleted><Year>2005</Year><Month>12</Month><Day>06</Day></DateCompleted><DateRevised><Year>2011</Year><Month>11</Month><Day>17</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0907-4449</ISSN><JournalIssue CitedMedium="Print"><Volume>61</Volume><Issue>Pt 9</Issue><PubDate><Year>2005</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Acta crystallographica. Section D, Biological crystallography</Title><ISOAbbreviation>Acta Crystallogr D Biol Crystallogr</ISOAbbreviation></Journal><ArticleTitle>Improving radiation-damage substructures for RIP.</ArticleTitle><Pagination><MedlinePgn>1227-37</MedlinePgn></Pagination><Abstract><AbstractText>Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nanao</LastName><ForeName>Max H</ForeName><Initials>MH</Initials><AffiliationInfo><Affiliation>EMBL, 6 Rue Jules Horowitz, 38042 Grenoble, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sheldrick</LastName><ForeName>George M</ForeName><Initials>GM</Initials></Author><Author ValidYN="Y"><LastName>Ravelli</LastName><ForeName>Raimond B G</ForeName><Initials>RB</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2005</Year><Month>08</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Acta Crystallogr D Biol Crystallogr</MedlineTA><NlmUniqueID>9305878</NlmUniqueID><ISSNLinking>0907-4449</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004220">Disulfides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004798">Enzymes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D007328">Insulin</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>53850-34-3</RegistryNumber><NameOfSubstance UI="C003427">thaumatin protein, plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.27.5</RegistryNumber><NameOfSubstance UI="D012259">Ribonuclease, Pancreatic</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.17</RegistryNumber><NameOfSubstance UI="D009113">Muramidase</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.21.36</RegistryNumber><NameOfSubstance UI="D010196">Pancreatic Elastase</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.21.4</RegistryNumber><NameOfSubstance UI="D014357">Trypsin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004220" MajorTopicYN="N">Disulfides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000528" MajorTopicYN="N">radiation effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004798" MajorTopicYN="N">Enzymes</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000528" MajorTopicYN="N">radiation effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007328" MajorTopicYN="N">Insulin</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000528" MajorTopicYN="N">radiation effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008722" MajorTopicYN="N">Methods</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015394" MajorTopicYN="N">Molecular Structure</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009113" MajorTopicYN="N">Muramidase</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000528" MajorTopicYN="N">radiation 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PubStatus="entrez"><Year>2005</Year><Month>9</Month><Day>1</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16131756</ArticleId><ArticleId IdType="pii">S0907444905019360</ArticleId><ArticleId IdType="doi">10.1107/S0907444905019360</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Rhône-Alpes</li></region><settlement><li>Grenoble</li></settlement></list><tree><noCountry><name sortKey="Ravelli, Raimond B G" sort="Ravelli, Raimond B G" uniqKey="Ravelli R" first="Raimond B G" last="Ravelli">Raimond B G. Ravelli</name><name sortKey="Sheldrick, George M" sort="Sheldrick, George M" uniqKey="Sheldrick G" first="George M" last="Sheldrick">George M. Sheldrick</name></noCountry><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Nanao, Max H" sort="Nanao, Max H" uniqKey="Nanao M" first="Max H" last="Nanao">Max H. Nanao</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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