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Yorodumi- PDB-2n5b: Structures of the OXIDIZED state of the mutant D24A of yeast thio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n5b | ||||||
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Title | Structures of the OXIDIZED state of the mutant D24A of yeast thioredoxin 1 | ||||||
Components | Thioredoxin-1 | ||||||
Keywords | OXIDOREDUCTASE / Redox Catalytic Activity / Water Cavity / Protein Hydration | ||||||
Function / homology | Function and homology information membrane fusion priming complex / protein deglutathionylation / vacuole inheritance / vacuole fusion, non-autophagic / disulfide oxidoreductase activity / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport ...membrane fusion priming complex / protein deglutathionylation / vacuole inheritance / vacuole fusion, non-autophagic / disulfide oxidoreductase activity / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / cell redox homeostasis / mitochondrial intermembrane space / protein transport / Golgi membrane / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Iqbal, A. / Moraes, A.H. / Valente, A.P. / Almeida, F.C.L. | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2015 Title: Structures of the reduced and oxidized state of the mutant D24A of yeast thioredoxin 1: insights into the mechanism for the closing of the water cavity. Authors: Iqbal, A. / Moraes, A.H. / Valente, A.P. / Almeida, F.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n5b.cif.gz | 605.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n5b.ent.gz | 508.6 KB | Display | PDB format |
PDBx/mmJSON format | 2n5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/2n5b ftp://data.pdbj.org/pub/pdb/validation_reports/n5/2n5b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11200.922 Da / Num. of mol.: 1 / Mutation: D24A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: TRX1, TRX2, YLR043C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22217 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: TORSION ANGLE SIMULATED ANNEALING |
-Sample preparation
Details | Contents: 850 uM [U-100% 13C; U-100% 15N] yTrx1D24A, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 850 uM / Component: yTrx1D24A-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.02 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR constraints | NOE constraints total: 1272 / NOE intraresidue total count: 502 / NOE long range total count: 197 / NOE medium range total count: 60 / NOE sequential total count: 261 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 85 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: lowest energy / Conformers calculated total number: 400 / Conformers submitted total number: 20 |