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Yorodumi- PDB-5cad: Crystal structure of the vicilin from Solanum melongena revealed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cad | ||||||
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Title | Crystal structure of the vicilin from Solanum melongena revealed existence of different anionic ligands in structurally similar pockets | ||||||
Components | SM80.1 Vicilin | ||||||
Keywords | PLANT PROTEIN / Solanaceae / Solanum melongena / 7S vicilin / SM80.1 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Solanum melongena (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å | ||||||
Authors | Jain, A. / Kumar, A. / Salunke, D.M. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Crystal structure of the vicilin from Solanum melongena reveals existence of different anionic ligands in structurally similar pockets Authors: Jain, A. / Kumar, A. / Salunke, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cad.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cad.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 5cad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cad_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 5cad_full_validation.pdf.gz | 473.9 KB | Display | |
Data in XML | 5cad_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 5cad_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/5cad ftp://data.pdbj.org/pub/pdb/validation_reports/ca/5cad | 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: 42643.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum melongena (plant) / Tissue: seed / References: UniProt: A0A158RFR1*PLUS |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-PCA / |
#5: 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: 2.58 Å3/Da / Density % sol: 52.33 % / Description: Hexagonal crystal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 50mM Tris-Cl, 1.5 M Sodium malonate, 10% Peg 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→22.71 Å / Num. obs: 70495 / % possible obs: 99.9 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.49→1.57 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.49→22.71 Å / Cross valid method: FREE R-VALUE / σ(F): 23
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Solvent computation | Bsol: 59.2503 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 67.63 Å2 / Biso mean: 21.2462 Å2 / Biso min: 1.05 Å2
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Refinement step | Cycle: final / Resolution: 1.49→22.71 Å
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Refine LS restraints |
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Xplor file |
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