Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K.
Identifieur interne : 004B56 ( Main/Exploration ); précédent : 004B55; suivant : 004B57Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K.
Auteurs : B A Fields [Australie] ; H H Bartsch ; H D Bartunik ; F. Cordes ; J M Guss ; H C FreemanSource :
- Acta crystallographica. Section D, Biological crystallography [ 0907-4449 ] ; 1994.
Abstract
The structure of the copper protein plastocyanin from poplar leaves (Populus nigra var. italica) at 173 K has been subjected to two independent refinements, using a single set of synchrotron X-ray data at 1.6 A resolution. Energy-restrained refinement using the program EREF resulted in lower root-mean-square deviations from ideal geometry (e.g. 0.011 A for bond lengths) but a higher residual R (0.153) than restrained least-squares refinement using the program PROLSQ (0.014 A, 0.132). Electron-density difference maps in both refinements provided evidence for disorder at some side chains and solvent atoms, and the PROLSQ refinement made allowance for this disorder. The number of solvent sites identified at the 4sigma(rho) level was 171 in the EREF refinement and 189 in the PROLSQ refinement; 159 of the solvent sites are common to both refinements within 1 A. The root-mean-square differences between the atomic positions produced by the two refinements are 0.08 A for C(alpha) atoms, 0.08 A for backbone atoms and 0.12 A for all non-H atoms (excluding six obvious outliers) of the protein molecule. The two sets of Cu-ligand bond lengths differ by up to 0.07 A, and the ligand-Cu-ligand angles by up to 7 degrees. At 173 K the volume of the unit cell is 4.2% smaller than at 295 K. Greater order in the solvent region is indicated by the location of 79 more solvent sites, the identification of extensive networks of hydrogen-bonded rings of solvent molecules, and a general decrease in the thermal parameters. Within the unit cell, the protein molecules are significantly translated and rotated from their positions at ambient temperature. An important structural change at low temperature is a 180 degrees flip of the peptide group at Ser48-Gly49. Nearly all other significant differences between the structures of the protein at 173 and 295 K occur at exposed side chains. If the backbone atoms in the 173 and 295 K structures are superposed, excluding atoms involved in the peptide flip, the root-mean- square difference between the positions of 393 atoms is 0.25 A. Two internal water molecules, not included in previous descriptions of poplar plastocyanin, have been located. The plastocyanin Cu-site geometry at 173 K is not significantly different from that at 295 K. If plastocyanin undergoes a change in Cu-site geometry at low temperature, as has been suggested on the basis of resonance Raman spectroscopic evidence, then the change is not detected within the limits of precision of the present results.
DOI: 10.1107/S0907444994003021
PubMed: 15299368
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Cordes</name></author><author><name sortKey="Guss, J M" sort="Guss, J M" uniqKey="Guss J" first="J M" last="Guss">J M Guss</name></author><author><name sortKey="Freeman, H C" sort="Freeman, H C" uniqKey="Freeman H" first="H C" last="Freeman">H C Freeman</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1994">1994</date><idno type="RBID">pubmed:15299368</idno><idno type="pmid">15299368</idno><idno type="doi">10.1107/S0907444994003021</idno><idno type="wicri:Area/Main/Corpus">004B23</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">004B23</idno><idno type="wicri:Area/Main/Curation">004B23</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">004B23</idno><idno type="wicri:Area/Main/Exploration">004B23</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K.</title><author><name sortKey="Fields, B A" sort="Fields, B A" uniqKey="Fields B" first="B A" last="Fields">B A Fields</name><affiliation wicri:level="4"><nlm:affiliation>Department of Inorganic Chemistry, University of Sydney, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Inorganic Chemistry, University of Sydney</wicri:regionArea><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName><orgName type="university">Université de Sydney</orgName></affiliation></author><author><name sortKey="Bartsch, H H" sort="Bartsch, H H" uniqKey="Bartsch H" first="H H" last="Bartsch">H H Bartsch</name></author><author><name sortKey="Bartunik, H D" sort="Bartunik, H D" uniqKey="Bartunik H" first="H D" last="Bartunik">H D Bartunik</name></author><author><name sortKey="Cordes, F" sort="Cordes, F" uniqKey="Cordes F" first="F" last="Cordes">F. Cordes</name></author><author><name sortKey="Guss, J M" sort="Guss, J M" uniqKey="Guss J" first="J M" last="Guss">J M Guss</name></author><author><name sortKey="Freeman, H C" sort="Freeman, H C" uniqKey="Freeman H" first="H C" last="Freeman">H C Freeman</name></author></analytic><series><title level="j">Acta crystallographica. Section D, Biological crystallography</title><idno type="ISSN">0907-4449</idno><imprint><date when="1994" type="published">1994</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The structure of the copper protein plastocyanin from poplar leaves (Populus nigra var. italica) at 173 K has been subjected to two independent refinements, using a single set of synchrotron X-ray data at 1.6 A resolution. Energy-restrained refinement using the program EREF resulted in lower root-mean-square deviations from ideal geometry (e.g. 0.011 A for bond lengths) but a higher residual R (0.153) than restrained least-squares refinement using the program PROLSQ (0.014 A, 0.132). Electron-density difference maps in both refinements provided evidence for disorder at some side chains and solvent atoms, and the PROLSQ refinement made allowance for this disorder. The number of solvent sites identified at the 4sigma(rho) level was 171 in the EREF refinement and 189 in the PROLSQ refinement; 159 of the solvent sites are common to both refinements within 1 A. The root-mean-square differences between the atomic positions produced by the two refinements are 0.08 A for C(alpha) atoms, 0.08 A for backbone atoms and 0.12 A for all non-H atoms (excluding six obvious outliers) of the protein molecule. The two sets of Cu-ligand bond lengths differ by up to 0.07 A, and the ligand-Cu-ligand angles by up to 7 degrees. At 173 K the volume of the unit cell is 4.2% smaller than at 295 K. Greater order in the solvent region is indicated by the location of 79 more solvent sites, the identification of extensive networks of hydrogen-bonded rings of solvent molecules, and a general decrease in the thermal parameters. Within the unit cell, the protein molecules are significantly translated and rotated from their positions at ambient temperature. An important structural change at low temperature is a 180 degrees flip of the peptide group at Ser48-Gly49. Nearly all other significant differences between the structures of the protein at 173 and 295 K occur at exposed side chains. If the backbone atoms in the 173 and 295 K structures are superposed, excluding atoms involved in the peptide flip, the root-mean- square difference between the positions of 393 atoms is 0.25 A. Two internal water molecules, not included in previous descriptions of poplar plastocyanin, have been located. The plastocyanin Cu-site geometry at 173 K is not significantly different from that at 295 K. If plastocyanin undergoes a change in Cu-site geometry at low temperature, as has been suggested on the basis of resonance Raman spectroscopic evidence, then the change is not detected within the limits of precision of the present results.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">15299368</PMID><DateCompleted><Year>2005</Year><Month>02</Month><Day>14</Day></DateCompleted><DateRevised><Year>2007</Year><Month>07</Month><Day>24</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0907-4449</ISSN><JournalIssue CitedMedium="Print"><Volume>50</Volume><Issue>Pt 5</Issue><PubDate><Year>1994</Year><Month>Sep</Month><Day>01</Day></PubDate></JournalIssue><Title>Acta crystallographica. Section D, Biological crystallography</Title><ISOAbbreviation>Acta Crystallogr D Biol Crystallogr</ISOAbbreviation></Journal><ArticleTitle>Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K.</ArticleTitle><Pagination><MedlinePgn>709-30</MedlinePgn></Pagination><Abstract><AbstractText>The structure of the copper protein plastocyanin from poplar leaves (Populus nigra var. italica) at 173 K has been subjected to two independent refinements, using a single set of synchrotron X-ray data at 1.6 A resolution. Energy-restrained refinement using the program EREF resulted in lower root-mean-square deviations from ideal geometry (e.g. 0.011 A for bond lengths) but a higher residual R (0.153) than restrained least-squares refinement using the program PROLSQ (0.014 A, 0.132). Electron-density difference maps in both refinements provided evidence for disorder at some side chains and solvent atoms, and the PROLSQ refinement made allowance for this disorder. The number of solvent sites identified at the 4sigma(rho) level was 171 in the EREF refinement and 189 in the PROLSQ refinement; 159 of the solvent sites are common to both refinements within 1 A. The root-mean-square differences between the atomic positions produced by the two refinements are 0.08 A for C(alpha) atoms, 0.08 A for backbone atoms and 0.12 A for all non-H atoms (excluding six obvious outliers) of the protein molecule. The two sets of Cu-ligand bond lengths differ by up to 0.07 A, and the ligand-Cu-ligand angles by up to 7 degrees. At 173 K the volume of the unit cell is 4.2% smaller than at 295 K. Greater order in the solvent region is indicated by the location of 79 more solvent sites, the identification of extensive networks of hydrogen-bonded rings of solvent molecules, and a general decrease in the thermal parameters. Within the unit cell, the protein molecules are significantly translated and rotated from their positions at ambient temperature. An important structural change at low temperature is a 180 degrees flip of the peptide group at Ser48-Gly49. Nearly all other significant differences between the structures of the protein at 173 and 295 K occur at exposed side chains. If the backbone atoms in the 173 and 295 K structures are superposed, excluding atoms involved in the peptide flip, the root-mean- square difference between the positions of 393 atoms is 0.25 A. Two internal water molecules, not included in previous descriptions of poplar plastocyanin, have been located. The plastocyanin Cu-site geometry at 173 K is not significantly different from that at 295 K. If plastocyanin undergoes a change in Cu-site geometry at low temperature, as has been suggested on the basis of resonance Raman spectroscopic evidence, then the change is not detected within the limits of precision of the present results.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fields</LastName><ForeName>B A</ForeName><Initials>BA</Initials><AffiliationInfo><Affiliation>Department of Inorganic Chemistry, University of Sydney, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bartsch</LastName><ForeName>H H</ForeName><Initials>HH</Initials></Author><Author ValidYN="Y"><LastName>Bartunik</LastName><ForeName>H D</ForeName><Initials>HD</Initials></Author><Author ValidYN="Y"><LastName>Cordes</LastName><ForeName>F</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Guss</LastName><ForeName>J M</ForeName><Initials>JM</Initials></Author><Author ValidYN="Y"><LastName>Freeman</LastName><ForeName>H C</ForeName><Initials>HC</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Acta Crystallogr D Biol Crystallogr</MedlineTA><NlmUniqueID>9305878</NlmUniqueID><ISSNLinking>0907-4449</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1994</Year><Month>9</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1994</Year><Month>9</Month><Day>1</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1994</Year><Month>9</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15299368</ArticleId><ArticleId IdType="doi">10.1107/S0907444994003021</ArticleId><ArticleId IdType="pii">S0907444994003021</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Australie</li></country><region><li>Nouvelle-Galles du Sud</li></region><settlement><li>Sydney</li></settlement><orgName><li>Université de Sydney</li></orgName></list><tree><noCountry><name sortKey="Bartsch, H H" sort="Bartsch, H H" uniqKey="Bartsch H" first="H H" last="Bartsch">H H Bartsch</name><name sortKey="Bartunik, H D" sort="Bartunik, H D" uniqKey="Bartunik H" first="H D" last="Bartunik">H D Bartunik</name><name sortKey="Cordes, F" sort="Cordes, F" uniqKey="Cordes F" first="F" last="Cordes">F. Cordes</name><name sortKey="Freeman, H C" sort="Freeman, H C" uniqKey="Freeman H" first="H C" last="Freeman">H C Freeman</name><name sortKey="Guss, J M" sort="Guss, J M" uniqKey="Guss J" first="J M" last="Guss">J M Guss</name></noCountry><country name="Australie"><region name="Nouvelle-Galles du Sud"><name sortKey="Fields, B A" sort="Fields, B A" uniqKey="Fields B" first="B A" last="Fields">B A Fields</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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