+Open data
-Basic information
Entry | Database: PDB / ID: 2evx | ||||||
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Title | Crystal structure of pumpkin seed globulin | ||||||
Components | 11S globulin beta subunit | ||||||
Keywords | PLANT PROTEIN / cucubitin / pumpkin seed storage globulin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cucurbita maxima (winter squash) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Itoh, T. / Fukuda, T. / Mikami, B. / Utsumi, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Pumpkin Seed Globulin Authors: Itoh, T. / Fukuda, T. / Mikami, B. / Utsumi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2evx.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2evx.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 2evx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2evx_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 2evx_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 2evx_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 2evx_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/2evx ftp://data.pdbj.org/pub/pdb/validation_reports/ev/2evx | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52392.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cucurbita maxima (winter squash) / Tissue: seed / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13744 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 30, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 17371 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 18.7 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.374 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→14.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4657310.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.2264 Å2 / ksol: 0.364002 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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