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This is the most recent MD file of the STRENDA DB structure
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| # STRENDA DB | ||
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| ## Administration | ||
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| ## Data | ||
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| ### Publication | ||
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| This is the publication that includes the experimental results of an enzyme kinetics characterization. | ||
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| * **Title** | ||
| * type: string | ||
| * description: title of the publication | ||
| * DOI | ||
| * type: string | ||
| * description: identifier of the publication | ||
| * PMID | ||
| * type: string | ||
| * description: identifier of the publication as indexed in PubMed | ||
| * Author | ||
| * type: Author | ||
| * Multiple: true | ||
| * Experiment | ||
| * type: Experiment | ||
| * Multiple: true | ||
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| ### Author | ||
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| * **Name** | ||
| * type: string | ||
| * description: name of the author. Nomenclature: Family name initials first name | ||
| * Affiliation | ||
| * type: string | ||
| * description: name of organizaton, department, city, country | ||
| * type: string | ||
| * description: email address | ||
| * ORCID | ||
| * type: string | ||
| * description: ORCID idenfier | ||
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| ### Experiment | ||
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| * Name of Experiment | ||
| * type: string | ||
| * description: name of the experiment, just for internal purposes | ||
| * Type of Assay | ||
| * type: string | ||
| * description: name of the assay | ||
| * Direction of the Assay | ||
| * type: string | ||
| * description: | ||
| * Definition of the compound monitored | ||
| * type: string | ||
| * description: | ||
| * Continuously monitored | ||
| * type: string | ||
| * description: selection of the stopping procedure | ||
| * type: string | ||
| * description: other | ||
| * type: string | ||
| * Directly monitored | ||
| * type: string | ||
| * Protein Assay | ||
| * type: ProteinDescription | ||
| * Multiple: false | ||
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| ### ProteinDescription | ||
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| * UniProtKB AC | ||
| * type: string | ||
| * description: identifier obtained from UniProtKB | ||
| * Protein name | ||
| * type: string | ||
| * description: name of the protein as of UniProtKB | ||
| * Protein Sequence | ||
| * type: SequenceModifications | ||
| * description: amino acid sequence as from UniProtKB | ||
| * Posttranslational modifications | ||
| * type: PosttranslationalModifications | ||
| * Protein Source | ||
| * type: ProteinSource | ||
| * Reaction | ||
| * type: ProteinReaction | ||
| * Protein characterization | ||
| * type: Dataset | ||
| * Multiple: true | ||
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| ### ProteinSource | ||
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| * Expression system | ||
| * type: string | ||
| * description: description of expression system if heterologously expressed | ||
| * Organism | ||
| * type: string | ||
| * description: as in UniProtKB provided, name of organism | ||
| * Taxon ID | ||
| * type: string | ||
| * description: ID as obtained from NCBI Taxonomy | ||
| * Strain | ||
| * type: string | ||
| * description: name or identifier of the strain | ||
| * Cell Type | ||
| * type: string | ||
| * description: determination of the cell in which the protein is expressed | ||
| * Tissue | ||
| * type: string | ||
| * description: determination of the tissue, ideally BTO is used | ||
| * Localization | ||
| * type: string | ||
| * description: determination of the localization (membran, cytosol, etc.) | ||
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| ### SequenceModifications | ||
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| * Sequence modification | ||
| * type: string | ||
| * description: modified amino acid sequence | ||
| * Specification of the type of modification | ||
| * type: string | ||
| * description: description of the types of modifications | ||
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| ### PosttranslationalModifications | ||
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| * Determination of PTM | ||
| * type: string | ||
| * description: Phosphorylation, Glycosylation, Acetylation, Hydroxylation, Methylation, Other | ||
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| ### ProteinReaction | ||
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| * EC number | ||
| * type: string | ||
| * description: EC number obtained from ExplorEnz | ||
| * Reaction as in ExplorEnz | ||
| * type: string | ||
| * description: reaction as described in ExplorEnz | ||
| * Comment | ||
| * type: string | ||
| * description: comment on the protein reaction if not properly described in ExplorEnz | ||
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| ### Dataset | ||
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| * Name | ||
| * type: string | ||
| * description: name of the dataset | ||
| * Assay conditions | ||
| * type: AssayConditions | ||
| * Multiple: true | ||
| * Results Set | ||
| * type: ResultsSet | ||
| * Multiple: true | ||
| * DOI | ||
| * type: string | ||
| * description: DOI of the dataset | ||
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| ### AssayConditions | ||
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| * Small Assay Components | ||
| * type: Small\_Assay\_Components | ||
| * description: description of the compound used in the assay | ||
| * Macromolecular Components | ||
| * type: Macromolecular\_Components | ||
| * description: description of the macromolecular components | ||
| * Concentration of the assayed protein | ||
| * type: string | ||
| * description: value with unit | ||
| * Description of concentration measurement | ||
| * type: string | ||
| * description: free text field | ||
| * pH | ||
| * type: string | ||
| * description: value and unit | ||
| * pD | ||
| * type: string | ||
| * description: value and unit | ||
| * Temperature | ||
| * type: string | ||
| * description: value and unit, K and Celsius | ||
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| ### Small\_Assay\_Components | ||
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| * Role | ||
| * type: Role\_of\_Component | ||
| * description: role in the assay, i.e. substrate, product, etc. | ||
| * Initial concentration - fixed | ||
| * type: string | ||
| * description: unit, value | ||
| * Initial concentration - varied | ||
| * type: string | ||
| * description: concentration range, value, unit | ||
| * Compound name | ||
| * type: string | ||
| * description: name as obtained from PubChem | ||
| * InChi | ||
| * type: string | ||
| * description: InChi string | ||
| * IUPAC | ||
| * type: string | ||
| * description: IUPAC name | ||
| * ChEBI ID | ||
| * type: string | ||
| * description: identifier | ||
| * PubChem CID | ||
| * type: string | ||
| * description: identifier | ||
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| ### Macromolecular\_Components | ||
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| * Role | ||
| * type: Role\_of\_Component | ||
| * description: role in the assay, i.e. substrate, product, etc. | ||
| * Initial concentration - fixed | ||
| * type: string | ||
| * description: unit, value | ||
| * Initial concentration - varied | ||
| * type: string | ||
| * description: concentration range, value, unit | ||
| * Class | ||
| * type: Class | ||
| * description: protein, carbohydrate, DNA, RNA, etc. | ||
| * Compound name | ||
| * type: string | ||
| * description: name as obtained from PubChem | ||
| * InChi | ||
| * type: string | ||
| * description: InChi string | ||
| * IUPAC | ||
| * type: string | ||
| * description: IUPAC name | ||
| * Database used | ||
| * type: string | ||
| * description: name of the database | ||
| * Identifier | ||
| * type: string | ||
| * description: identifier | ||
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| ### Role\_of\_Component | ||
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| * Substrate | ||
| * type: string | ||
| * description: substrate of chemical reaction | ||
| * Product | ||
| * type: string | ||
| * description: production of chemical reaction | ||
| * Inhibitor | ||
| * type: string | ||
| * description: component that inhibits the chemical reaction | ||
| * Activator | ||
| * type: string | ||
| * description: component that activates/enhances the chemical reaction | ||
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| ### Class | ||
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| * Protein | ||
| * type: string | ||
| * Carbohydrate | ||
| * type: string | ||
| * DNA | ||
| * type: string | ||
| * RNA | ||
| * type: string | ||
| * Lipid | ||
| * type: string | ||
| * Other | ||
| * type: string | ||
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| ### ResultsSet | ||
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| * Initial Kinetic Parameters | ||
| * type: Initial\_Kinetics\_Parameters | ||
| * description: Km, kcat, V, kcat/Km, V/Km | ||
| * Activation | ||
| * type: Activation | ||
| * Inhibition | ||
| * type: Inhibition | ||
| * | ||
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| ### Initial\_Kinetics\_Parameters | ||
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| * Km | ||
| * type: string | ||
| * descriptor: value, SE, unit | ||
| * kcat | ||
| * type: string | ||
| * descriptor: value, SE, unit | ||
| * V | ||
| * type: string | ||
| * descriptor: value, SE, unit | ||
| * kcat/Km | ||
| * type: string | ||
| * descriptor: value, SE, unit | ||
| * V/Km | ||
| * type: string | ||
| * descriptor: value, SE, unit | ||
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| ### Activation | ||
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| * Affinity constant | ||
| * type: string | ||
| * descriptor: value, SE, unit, true or apparent | ||
| * Reaction velocity | ||
| * no activator | ||
| * type: string | ||
| * description: velocity without activator | ||
| * at max. concentration | ||
| * type: string | ||
| * description: velocity at maximum concentration of activator | ||
| * Saturation | ||
| * type: string | ||
| * description: statement whether the concentration was saturating or not | ||
| * Influence on substrate MM kinetics | ||
| * Km no activator | ||
| * type: string | ||
| * description: Value, SE, Unit, true/apparent | ||
| * at max. concentration | ||
| * type: string | ||
| * description: Value, SE, Unit, true/apparent | ||
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| ### Inhibition | ||
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| * Reversibility\_yes | ||
| * type: string | ||
| * description: inhbition type - competitive, uncompetitive, mixed, kic, SE, Unit, Math function | ||
| * Reversibility\_no | ||
| * type: string | ||
| * description: ki, SE, Unit, Comment |