+Open data
-Basic information
Entry | Database: PDB / ID: 2e9q | ||||||
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Title | Recombinant pro-11S globulin of pumpkin | ||||||
Components | 11S globulin subunit beta | ||||||
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 / MIR / Resolution: 2.2 Å | ||||||
Authors | Fukuda, T. / Prak, K. / Itoh, T. / Masuda, T. / Maruyama, N. / Mikami, B. / Utsumi, S. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2010 Title: Conservation and divergence on plant seed 11S globulins based on crystal structures. Authors: Tandang-Silvas, M.R. / Fukuda, T. / Fukuda, C. / Prak, K. / Cabanos, C. / Kimura, A. / Itoh, T. / Mikami, B. / Utsumi, S. / Maruyama, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e9q.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e9q.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 2e9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/2e9q ftp://data.pdbj.org/pub/pdb/validation_reports/e9/2e9q | HTTPS FTP |
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-Related structure data
Related structure data | 2d5fC 2d5hC 3kglC 3kscC 2evxS 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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2 |
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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) / 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 | ChemComp-PO4 / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Sequence details | THE DEPOSITORS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2M NaCl, 0.1M Na/K phosphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Dec 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 28317 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 122 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 5.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 2EVX Resolution: 2.2→14.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6082737.77 / 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: 56.369 Å2 / ksol: 0.334128 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→14.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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