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- PDB-5vf5: Crystal structure of the vicilin from Solanum melongena, re-refinement -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vf5 | ||||||||||||
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Title | Crystal structure of the vicilin from Solanum melongena, re-refinement | ||||||||||||
![]() | SM80.1 Vicilin | ||||||||||||
![]() | PLANT PROTEIN / 7S VICILIN SM80.1 PLANT PROTEIN SEQUENCE ASSIGNMENT RE-REFINEMENT | ||||||||||||
Function / homology | ![]() Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Porebski, P.J. / Wlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B. | ||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() 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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Remark 0 | THIS ENTRY 5VF5 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5CAD, DETERMINED BY A. ...THIS ENTRY 5VF5 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5CAD, DETERMINED BY A.JAIN,A.KUMAR,D.M.SALUNKE |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.8 KB | Display | ![]() |
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PDB format | ![]() | 144.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.9 KB | Display | ![]() |
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Full document | ![]() | 470.7 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vehC ![]() 5vepC ![]() 5veqC ![]() 5verC ![]() 5vetC ![]() 5vf2C ![]() 5vgaC ![]() 5cadS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48761.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 357 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / |
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#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-CU / |
#5: Chemical | ChemComp-PEG / |
#6: Chemical | ChemComp-MLI / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5CAD |
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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 / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
Software | Name: REFMAC / Version: 5.8.0158 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 5CAD Resolution: 1.49→22.71 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.969 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.839 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→22.71 Å
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Refine LS restraints |
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