[English] 日本語
Yorodumi- PDB-1n3o: Pterocarcpus angolensis lectin in complex with alpha-methyl glucose -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n3o | ||||||
---|---|---|---|---|---|---|---|
Title | Pterocarcpus angolensis lectin in complex with alpha-methyl glucose | ||||||
Components | lectin PAL | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / carbohydrate recognition / glucose | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pterocarpus angolensis (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Loris, R. / Imberty, A. / Beeckmans, S. / Van Driessche, E. / Read, J.S. / Bouckaert, J. / De Greve, H. / Buts, L. / Wyns, L. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Crystal structure of Pterocarpus angolensis lectin in complex with glucose, sucrose, and turanose Authors: Loris, R. / Imberty, A. / Beeckmans, S. / Van Driessche, E. / Read, J.S. / Bouckaert, J. / De Greve, H. / Buts, L. / Wyns, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n3o.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n3o.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n3o_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1n3o_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 1n3o_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 1n3o_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n3o ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n3o | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27575.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pterocarpus angolensis (plant) / References: UniProt: Q8GSD2 #2: Sugar | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 52.93 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ca-acetate, PEG-8000, Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.45 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 2000 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. all: 39215 / Num. obs: 39215 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.44 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.43 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.311 / Num. unique all: 3190 / % possible all: 80.5 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 173945 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 80.5 % / Num. unique obs: 3190 / Num. measured obs: 13215 / Mean I/σ(I) obs: 4.65 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.186 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.222 |