Dataset Information

Production, purification, crystallization and structure determination of H-1 Parvovirus.

ABSTRACT: Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7?Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a=255.4, b=350.4, c=271.6?Å, ?=90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined.

SUBMITTER: Halder S

PROVIDER: S-EPMC3509992 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Production, purification, crystallization and structure determination of H-1 Parvovirus.

Halder Sujata S Nam Hyun Joo HJ Govindasamy Lakshmanan L Vogel Michèle M Dinsart Christiane C Salomé Nathalie N McKenna Robert R Agbandje-McKenna Mavis M

Acta crystallographica. Section F, Structural biology and crystallization communications 20121128 Pt 12

Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a=255.4, b=350.4, c=271.6 Å, β=90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined. ...[more]

PMID: 23192051

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Project description:MotivationX-ray crystallography-based protein structure determination, which accounts for majority of solved structures, is characterized by relatively low success rates. One solution is to build tools which support selection of targets that are more likely to crystallize. Several in silico methods that predict propensity of diffraction-quality crystallization from protein chains were developed. We show that the quality of their predictions drops when applied to more recent crystallization trails, which calls for new solutions. We propose a novel approach that alleviates drawbacks of the existing methods by using a recent dataset and improved protocol to annotate progress along the crystallization process, by predicting the success of the entire process and steps which result in the failed attempts, and by utilizing a compact and comprehensive set of sequence-derived inputs to generate accurate predictions.ResultsThe proposed PPCpred (predictor of protein Production, Purification and Crystallization) predict propensity for production of diffraction-quality crystals, production of crystals, purification and production of the protein material. PPCpred utilizes comprehensive set of inputs based on energy and hydrophobicity indices, composition of certain amino acid types, predicted disorder, secondary structure and solvent accessibility, and content of certain buried and exposed residues. Our method significantly outperforms alignment-based predictions and several modern crystallization propensity predictors. Receiver operating characteristic (ROC) curves show that PPCpred is particularly useful for users who desire high true positive (TP) rates, i.e. low rate of mispredictions for solvable chains. Our model reveals several intuitive factors that influence the success of individual steps and the entire crystallization process, including the content of Cys, buried His and Ser, hydrophobic/hydrophilic segments and the number of predicted disordered segments.Availabilityhttp://biomine.ece.ualberta.ca/PPCpred/.Contactlkurgan@ece.ualberta.ca.

Dataset Information

Production, purification, crystallization and structure determination of H-1 Parvovirus.

Publications

Production, purification, crystallization and structure determination of H-1 Parvovirus.

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