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Harris, Mark R.
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Publications (3 of 3) Show all publications
Kleywegt, G. J. & Harris, M. R. (2007). ValLigURL: a server for ligand-structure comparison and validation. Acta Crystallographica Section D: Biological Crystallography, 63, 935-938
Open this publication in new window or tab >>ValLigURL: a server for ligand-structure comparison and validation
2007 (English)In: Acta Crystallographica Section D: Biological Crystallography, ISSN 0907-4449, E-ISSN 1399-0047, Vol. 63, p. 935-938Article in journal (Refereed) Published
Abstract [en]

A new web-based tool called ValLigURL is described. It can be used by practising crystallographers to validate the geometry of a ligand and to compare the conformation of a ligand with all instances of that ligand in the structural database (wwPDB). In addition, it can be used by structural bioinformaticians to survey the quality or conformational diversity of any ligand across the entire structural database. The server is freely accessible at the URL http://eds.bmc.uu.se/eds/valligurl.php.

Keywords
Computational Biology/*methods, Databases; Factual, Internet, Ligands, Models; Molecular, Molecular Conformation, Mycobacterium tuberculosis/chemistry, NADP/chemistry, Reproducibility of Results
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-13666 (URN)10.1107/S090744490703315X (DOI)000248078400011 ()17642521 (PubMedID)
Available from: 2008-06-05 Created: 2008-06-05 Last updated: 2017-12-11Bibliographically approved
Kleywegt, G. J., Harris, M. R., Zou, J. Y., Taylor, T. C., Wählby, A. & Jones, T. A. (2004). The Uppsala Electron-Density Server. Acta Crystallographica Section D: Biological Crystallography, 60(Pt 12 Pt 1), 2240-2249
Open this publication in new window or tab >>The Uppsala Electron-Density Server
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2004 (English)In: Acta Crystallographica Section D: Biological Crystallography, ISSN 0907-4449, E-ISSN 1399-0047, Vol. 60, no Pt 12 Pt 1, p. 2240-2249Article in journal (Refereed) Published
Abstract [en]

The Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) is a web-based facility that provides access to electron-density maps and statistics concerning the fit of crystal structures and their maps. Maps are available for approximately 87% of the crystallographic Protein Data Bank (PDB) entries for which structure factors have been deposited and for which straightforward map calculations succeed in reproducing the published R value to within five percentage points. Here, an account is provided of the methods that are used to generate the information contained in the server. Some of the problems that are encountered in the map-generation process as well as some spin-offs of the project are also discussed.

Keywords
Computational Biology, Crystallography; X-Ray, Databases; Protein, Electrons, Internet, Proteins/chemistry, Reproducibility of Results, Research Support; Non-U.S. Gov't, Software, Temperature
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-71671 (URN)15572777 (PubMedID)
Available from: 2006-12-15 Created: 2006-12-15 Last updated: 2017-11-21Bibliographically approved
Becker, D., Braet, C., Brumer, H., Claeyssens, M., Divne, C., Fagerström, V., . . . Wohlfart, G. (2001). Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei CeI7A and its E223S/A224H/L225V/T226A/D262G mutant. Biochemical Journal, 356, 19-30
Open this publication in new window or tab >>Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei CeI7A and its E223S/A224H/L225V/T226A/D262G mutant
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2001 (English)In: Biochemical Journal, Vol. 356, p. 19-30Article in journal (Refereed) Published
Abstract [en]

The crystal structures of Family 7 glycohydrolases suggest that a histidine residue near the acid/base catalyst could account for the higher pH optimum of the Humicola insolens endoglucanase Cel7B, than the corresponding Trichoderma reesei enzymes. Modelling studies indicated that introduction of histidine at the homologous position in T. reesei Cel7A (Ala(224)) required additional changes to accommodate the bulkier histidine side chain. X-ray crystallography of the catalytic domain of the E223S/A224H/L225V/T226A/D262G mutant reveals that major differences from the wild-type are confined to the mutations themselves. The introduced histidine residue is in plane with its counterpart in H. insolens Cel7B, but is 1.0 A (=0.1 nm) closer to the acid/base Glu(217) residue, with a 3.1 A contact between N(epsilon2) and O(epsilon1). The pH variation of k(cat)/K(m) for 3,4-dinitrophenyl lactoside hydrolysis was accurately bell-shaped for both wild-type and mutant, with pK(1) shifting from 2.22+/-0.03 in the wild-type to 3.19+/-0.03 in the mutant, and pK(2) shifting from 5.99+/-0.02 to 6.78+/-0.02. With this poor substrate, the ionizations probably represent those of the free enzyme. The relative k(cat) for 2-chloro-4-nitrophenyl lactoside showed similar behaviour. The shift in the mutant pH optimum was associated with lower k(cat)/K(m) values for both lactosides and cellobiosides, and a marginally lower stability. However, k(cat) values for cellobiosides are higher for the mutant. This we attribute to reduced non-productive binding in the +1 and +2 subsites; inhibition by cellobiose is certainly relieved in the mutant. The weaker binding of cellobiose is due to the loss of two water-mediated hydrogen bonds.

Identifiers
urn:nbn:se:uu:diva-41987 (URN)
Available from: 2006-12-15 Created: 2006-12-15 Last updated: 2011-01-14
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