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Yorodumi- PDB-2dtd: Structure of Thermoplasma acidophilum aldohexose dehydrogenase (A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dtd | ||||||
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Title | Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free form | ||||||
Components | Glucose 1-dehydrogenase related protein | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yasutake, Y. / Nishiya, Y. / Tamura, N. / Tamura, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural Insights into Unique Substrate Selectivity of Thermoplasma acidophilumd-Aldohexose Dehydrogenase Authors: Yasutake, Y. / Nishiya, Y. / Tamura, N. / Tamura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dtd.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dtd.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/2dtd ftp://data.pdbj.org/pub/pdb/validation_reports/dt/2dtd | HTTPS FTP |
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-Related structure data
Related structure data | 2dteC 2dtxC 1gcoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homotetramer generated from the dimer in the asymmetric unit by the operations: x-y, -y, -z+1/3. |
-Components
#1: Protein | Mass: 29034.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0754 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9HK51, EC: 1.1.1.118 #2: Chemical | ChemComp-SO4 / #3: 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: 2.3 Å3/Da / Density % sol: 46.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 16% PEG 3350, 0.2M ammonium sulfate, 15% glycerol, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 32006 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.073 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 3137 / Rsym value: 0.283 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1gco Resolution: 2.1→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.12 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Total num. of bins used: 10
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