+Open data
-Basic information
Entry | Database: PDB / ID: 2eaa | ||||||
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Title | Crystal Structure of Adzuki Bean 7S Globulin-3 | ||||||
Components | 7S globulin-3 | ||||||
Keywords | PLANT PROTEIN / BETA BARREL / CUPIN SUPERFAMILY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vigna angularis (adzuki bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Fukuda, T. / Mikami, B. / Utsumi, S. | ||||||
Citation | Journal: J.Agric.Food Chem. / Year: 2008 Title: Characterization and crystallography of recombinant 7S globulins of Adzuki bean and structure-function relationships with 7S globulins of various crops. Authors: Fukuda, T. / Maruyama, N. / Salleh, M.R. / 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 | 2eaa.cif.gz | 248.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eaa.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 2eaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/2eaa ftp://data.pdbj.org/pub/pdb/validation_reports/ea/2eaa | HTTPS FTP |
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-Related structure data
Related structure data | 2ea7SC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49823.512 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vigna angularis (adzuki bean) / Gene: 7S-3 / Plasmid: pEAdzuki7S3 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: A4PIA0 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% MPD, 0.2M ammonium acetate, 0.1M Sodium citrate, 2.0M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-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 RAXIS V / Detector: IMAGE PLATE / Date: Oct 4, 2006 / Details: mirror |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 69062 / Num. obs: 69062 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.415 / Num. unique all: 6784 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EA7 Resolution: 2.25→15 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2656502.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.4143 Å2 / ksol: 0.351261 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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