+Open data
-Basic information
Entry | Database: PDB / ID: 7cov | ||||||
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Title | Potato D-enzyme, native (substrate free) | ||||||
Components | 4-alpha-glucanotransferase, chloroplastic/amyloplastic | ||||||
Keywords | TRANSFERASE / D-enzyme / disproportionating enzyme / potato / cycloamylose / Solanum tuberosum / PLANT PROTEIN | ||||||
Function / homology | Function and homology information amyloplast / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / chloroplast / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Solanum tuberosum (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Unno, H. / Imamura, K. | ||||||
Citation | Journal: Protein Sci. / Year: 2020 Title: Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato. Authors: Imamura, K. / Matsuura, T. / Nakagawa, A. / Kitamura, S. / Kusunoki, M. / Takaha, T. / Unno, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cov.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cov.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 7cov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cov_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7cov_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7cov_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 7cov_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/7cov ftp://data.pdbj.org/pub/pdb/validation_reports/co/7cov | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65021.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum tuberosum (potato) / Gene: DPEP / Production host: Escherichia coli (E. coli) / References: UniProt: Q06801, 4-alpha-glucanotransferase | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.43 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion / Details: 12% PEG 8000, 100 mM HEPES (pH 7.6), 100 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 26, 2004 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.36 Å / Num. obs: 49562 / % possible obs: 99.2 % / Redundancy: 7.3 % / CC1/2: 1 / Rrim(I) all: 0.032 / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 2→2.11 Å / Num. unique obs: 7039 / CC1/2: 0.996 / Rrim(I) all: 0.092 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→35.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.124 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.523 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.36 Å
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Refine LS restraints |
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LS refinement shell |
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