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Yorodumi- PDB-6zom: Oxidized thioredoxin 1 from the anaerobic bacteria Desulfovibrio ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zom | ||||||
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Title | Oxidized thioredoxin 1 from the anaerobic bacteria Desulfovibrio vulgaris Hildenborough | ||||||
Components | Thioredoxin | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin / desulfovibrio / enzyme / cystein / vulgaris / redox homeostasis / regulation / thiol / oxidized | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Garcin, E. / Bornet, O. / Nouailler, M. / Pieulle, L. / Guerlesquin, F. / Sebban-Kreuzer, C. | ||||||
Citation | Journal: Extremophiles / Year: 2021 Title: Glutamate optimizes enzymatic activity under high hydrostatic pressure in Desulfovibrio species: effects on the ubiquitous thioredoxin system. Authors: Gaussier, H. / Nouailler, M. / Champaud, E. / Garcin, E.B. / Sebban-Kreuzer, C. / Bornet, O. / Garel, M. / Tamburini, C. / Pieulle, L. / Dolla, A. / Pradel, N. #1: Journal: Biomol NMR Assign / Year: 2011 Title: 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough. Authors: Garcin, E.B. / Bornet, O. / Pieulle, L. / Guerlesquin, F. / Sebban-Kreuzer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zom.cif.gz | 581 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zom.ent.gz | 486.3 KB | Display | PDB format |
PDBx/mmJSON format | 6zom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zom_validation.pdf.gz | 481.8 KB | Display | wwPDB validaton report |
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Full document | 6zom_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6zom_validation.xml.gz | 94.5 KB | Display | |
Data in CIF | 6zom_validation.cif.gz | 115.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/6zom ftp://data.pdbj.org/pub/pdb/validation_reports/zo/6zom | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12275.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: oxidized / Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Gene: trx, DVU_1839 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72B01 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1.0 mM [U-99% 13C; U-99% 15N] Thioredoxin 1, 90% H2O/10% D2O Details: oxidized thioredoxin, [U-99% 13C; U-99% 15N], 1 mM; H2O 90%; D2O 10%; NaCl 100 mM; Potassium phosphate 50 mM Label: oxidized thioredoxin / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.0 mM / Component: Thioredoxin 1 / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Details: oxidized thioredoxin, [U-99% 13C; U-99% 15N], 1 mM; H2O 90%; D2O 10%; NaCl 100 mM; Potassium phosphate 50 mM Ionic strength: 100 mM / Ionic strength err: 1 / Label: oxidized thioredoxin / pH: 5.5 / PH err: 0.01 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 290 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz / Details: cryoprobe |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 7 | ||||||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |