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- PDB-1xi0: X-ray crystal structure of wild-type Xerocomus chrysenteron lectin XCL -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xi0 | ||||||
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Title | X-ray crystal structure of wild-type Xerocomus chrysenteron lectin XCL | ||||||
![]() | lectin | ||||||
![]() | SUGAR BINDING PROTEIN / beta sandwich / greek key motif | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Birck, C. / Damian, L. / Marty-Detraves, C. / Lougarre, A. / Schulze-Briese, C. / Koehl, P. / Fournier, D. / Paquereau, L. / Samama, J.P. | ||||||
![]() | ![]() Title: A new lectin family with structure similarity to actinoporins revealed by the crystal structure of Xerocomus chrysenteron lectin XCL Authors: Birck, C. / Damian, L. / Marty-Detraves, C. / Lougarre, A. / Schulze-Briese, C. / Koehl, P. / Fournier, D. / Paquereau, L. / Samama, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.2 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.9 KB | Display | ![]() |
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Full document | ![]() | 438.5 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1x99SC 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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Unit cell |
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Components on special symmetry positions |
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Details | the biological assembly is a tetramer generated from the dimer in the asymetric unit by the operation: -x, -y, z |
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Components
#1: Protein | Mass: 16031.808 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: ammonium sulfate, MES, zinc chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2002 |
Radiation | Monochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. all: 89122 / Num. obs: 20047 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.062 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 2010 / Rsym value: 0.272 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1x99 Resolution: 2→50 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.32 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.009
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