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Yorodumi- PDB-1nw2: The crystal structure of the mutant R82E of Thioredoxin from Alic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nw2 | ||||||
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Title | The crystal structure of the mutant R82E of Thioredoxin from Alicyclobacillus acidocaldarius | ||||||
Components | THIOREDOXIN | ||||||
Keywords | ELECTRON TRANSPORT / Thermostability / thioredoxin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Alicyclobacillus acidocaldarius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bartolucci, S. / De Simone, G. / Galdiero, S. / Improta, R. / Menchise, V. / Pedone, C. / Pedone, E. / Saviano, M. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2003 Title: An integrated structural and computational study of the thermostability of two thioredoxin mutants from Alicyclobacillus acidocaldarius Authors: Bartolucci, S. / De Simone, G. / Galdiero, S. / Improta, R. / Menchise, V. / Pedone, C. / Pedone, E. / Saviano, M. #1: Journal: Biochem.J. / Year: 1999 Title: Prediction and Experimental Testing of Bacillus acidocaldarius Thioredoxin Stability. Authors: Pedone, E. / Cannio, R. / Saviano, M. / Rossi, M. / Bartolucci, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nw2.cif.gz | 187.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nw2.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nw2 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nw2 | HTTPS FTP |
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-Related structure data
Related structure data | 1nswC 2trxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11557.211 Da / Num. of mol.: 8 / Mutation: R82E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria) Production host: Escherichia coli (E. coli) References: UniProt: P80579, thioredoxin-disulfide reductase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Peg 8000, calcium acetate, CACODYLATE, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9072 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9072 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 52158 / Num. obs: 52158 / % possible obs: 84.1 % / Observed criterion σ(I): 0 / Rsym value: 0.051 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.262 / % possible all: 85.7 |
Reflection | *PLUS Num. measured all: 234705 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 85.7 % / Rmerge(I) obs: 0.262 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2TRX Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |