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- PDB-4yld: The crystal structure of Sclerotium Rolfsii lectin variant 1 (SSR1) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yld | ||||||
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Title | The crystal structure of Sclerotium Rolfsii lectin variant 1 (SSR1) | ||||||
![]() | Sclerotium Rolfsii lectin variant 1 (SSR1) | ||||||
![]() | SUGAR BINDING PROTEIN / Lectin / carbohydrate-binding specificity | ||||||
Function / homology | Fungal fruit body lectin / Fungal fruit body lectin / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta / Lectin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kantsadi, A.L. / Peppa, V.I. / Leonidas, D.D. | ||||||
![]() | ![]() Title: Molecular Cloning, Carbohydrate Specificity and the Crystal Structure of Two Sclerotium rolfsii Lectin Variants. Authors: Peppa, V.I. / Venkat, H. / Kantsadi, A.L. / Inamdar, S.R. / Bhat, G.G. / Eligar, S. / Shivanand, A. / Chachadi, V.B. / Satisha, G.J. / Swamy, B.M. / Skamnaki, V.T. / Zographos, S.E. / Leonidas, D.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 57.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.4 KB | Display | ![]() |
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Full document | ![]() | 439.9 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16062.690 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MPD / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54178 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 25, 2013 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→13.84 Å / Num. all: 36020 / Num. obs: 36020 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rsym value: 0.044 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 5.5 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→13.84 Å
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Refine LS restraints |
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LS refinement shell |
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