+Open data
-Basic information
Entry | Database: PDB / ID: 4twm | |||||||||||||||
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Title | Crystal structure of dioscorin from Dioscorea japonica | |||||||||||||||
Components | Dioscorin 5 | |||||||||||||||
Keywords | PLANT PROTEIN / storage protein / carbonic anhydrase activity / dehydroascorbate reductase activity | |||||||||||||||
Function / homology | Function and homology information response to oxygen radical / monodehydroascorbate reductase (NADH) / monodehydroascorbate reductase (NADH) activity / cellular response to carbon dioxide / carbon utilization / nutrient reservoir activity / negative regulation of endopeptidase activity / L-ascorbic acid binding / cellular oxidant detoxification / antioxidant activity ...response to oxygen radical / monodehydroascorbate reductase (NADH) / monodehydroascorbate reductase (NADH) activity / cellular response to carbon dioxide / carbon utilization / nutrient reservoir activity / negative regulation of endopeptidase activity / L-ascorbic acid binding / cellular oxidant detoxification / antioxidant activity / positive regulation of phagocytosis / carbonic anhydrase / carbonate dehydratase activity / serine-type endopeptidase inhibitor activity / positive regulation of gene expression / protein homodimerization activity / zinc ion binding Similarity search - Function | |||||||||||||||
Biological species | Dioscorea japonica (Japanese yam) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.11 Å | |||||||||||||||
Authors | Xue, Y.L. / Miyakawa, T. / Nakamura, A. / Tanokura, M. | |||||||||||||||
Funding support | Japan, China, 4items
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Citation | Journal: Mol Plant / Year: 2015 Title: Yam Tuber Storage Protein Reduces Plant Oxidants Using the Coupled Reactions as Carbonic Anhydrase and Dehydroascorbate Reductase Authors: Xue, Y.L. / Miyakawa, T. / Nakamura, A. / Hatano, K. / Sawano, Y. / Tanokura, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4twm.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4twm.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 4twm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/4twm ftp://data.pdbj.org/pub/pdb/validation_reports/tw/4twm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28217.619 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscorea japonica (Japanese yam) / Gene: dio5 / Production host: Escherichia coli (E. coli) / References: UniProt: A7MAQ2 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 10 / Details: CAPS, lithium sulfate, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→20 Å / Num. obs: 31706 / % possible obs: 99.3 % / Redundancy: 7 % / Net I/σ(I): 39.3 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.11→19.6 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.094 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.485 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→19.6 Å
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Refine LS restraints |
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