[English] 日本語
Yorodumi- PDB-1xi0: X-ray crystal structure of wild-type Xerocomus chrysenteron lectin XCL -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xi0 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of wild-type Xerocomus chrysenteron lectin XCL | ||||||
Components | lectin | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Xerocomus chrysenteron (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Birck, C. / Damian, L. / Marty-Detraves, C. / Lougarre, A. / Schulze-Briese, C. / Koehl, P. / Fournier, D. / Paquereau, L. / Samama, J.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xi0.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xi0.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/1xi0 ftp://data.pdbj.org/pub/pdb/validation_reports/xi/1xi0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1x99SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | the biological assembly is a tetramer generated from the dimer in the asymetric unit by the operation: -x, -y, z |
-Components
#1: Protein | Mass: 16031.808 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xerocomus chrysenteron (fungus) / Plasmid: modified pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8WZC9 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.5 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1x99 Resolution: 2→50 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
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
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.009
|