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- PDB-1y2t: Crystal structure of the common edible mushroom (Agaricus bisporu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y2t | ||||||
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Title | Crystal structure of the common edible mushroom (Agaricus bisporus) lectin | ||||||
![]() | lectin![]() | ||||||
![]() | SUGAR BINDING PROTEIN / ABL / ![]() ![]() ![]() | ||||||
Function / homology | Fungal fruit body lectin / Fungal fruit body lectin / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carrizo, M.E. / Capaldi, S. / Perduca, M. / Irazoqui, F.J. / Nores, G.A. / Monaco, H.L. | ||||||
![]() | ![]() Title: The Antineoplastic Lectin of the Common Edible Mushroom (Agaricus bisporus) Has Two Binding Sites, Each Specific for a Different Configuration at a Single Epimeric Hydroxyl Authors: Carrizo, M.E. / Capaldi, S. / Perduca, M. / Irazoqui, F.J. / Nores, G.A. / Monaco, H.L. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Crystallization and preliminary X-ray study of the common edible mushroom (Agaricus bisporus) lectin Authors: Carrizo, M.E. / Irazoqui, F.J. / Lardone, R.D. / Nores, G.A. / Curtino, J.A. / Capaldi, S. / Perduca, M. / Monaco, H.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.9 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -x, y, 1/2-z |
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Components
#1: Protein | ![]() Mass: 16069.765 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.5 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Sodium formate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 24, 2002 / Details: Three-segment Pt-coated toroidal |
Radiation | Monochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→74.5 Å / Num. all: 53757 / Num. obs: 53757 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.047 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 7606 / Rsym value: 0.087 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.461 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→65.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /
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