+Open data
-Basic information
Entry | Database: PDB / ID: 7e9x | ||||||
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Title | Trehalase of Arabidopsis thaliana acid mutant -D380A | ||||||
Components | Trehalase | ||||||
Keywords | HYDROLASE / trehalase / GH37 / Arabidopsis thaliana / Oryza sativa / trehalose / trehalose 6-phosphate / glycoside hydrolase / enzyme kinetics / enzyme structure | ||||||
Function / homology | Function and homology information alpha,alpha-trehalase / trehalose catabolic process / alpha,alpha-trehalase activity / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Taguchi, Y. / Saburi, W. / Yu, J. / Imai, R. / Yao, M. / Mori, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: pH-dependent alteration of substrate specificity of plant trehalase and its molecular mechanism Authors: Taguchi, Y. / Saburi, W. / Yu, J. / Imai, R. / Yao, M. / Mori, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e9x.cif.gz | 562.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e9x.ent.gz | 369.8 KB | Display | PDB format |
PDBx/mmJSON format | 7e9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e9x_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7e9x_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7e9x_validation.xml.gz | 81.8 KB | Display | |
Data in CIF | 7e9x_validation.cif.gz | 117.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/7e9x ftp://data.pdbj.org/pub/pdb/validation_reports/e9/7e9x | HTTPS FTP |
-Related structure data
Related structure data | 7e9uSC 7eawC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 65022.859 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: A predicted N-terminal transmembrane region (Met1-Leu63) was eliminated. Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TRE1, At4g24040, T19F6.15, T19F6.30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9SU50, alpha,alpha-trehalase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10 mM Tre6P, 0.1 M sodium chloride and 20% PEG3400. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→41.55 Å / Num. obs: 169902 / % possible obs: 99.8 % / Redundancy: 6.82 % / Biso Wilson estimate: 28.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.34 |
Reflection shell | Resolution: 1.88→1.95 Å / Num. unique obs: 27135 / CC1/2: 0.838 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7e9u Resolution: 1.88→41.55 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5987 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→41.55 Å
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Refine LS restraints |
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LS refinement shell |
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