[English] 日本語
Yorodumi- PDB-2gmp: Metal-free (apo) P. angolensis seed lectin in complex with GlcNAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gmp | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Metal-free (apo) P. angolensis seed lectin in complex with GlcNAC-beta(1-2)Man | ||||||||||||
Components | lectin | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / legume lectin / metal-free lectin / sugar complex / GlcNAc-beta(1-2)Man / beta sandwich | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pterocarpus angolensis (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||||||||
Authors | Garcia-Pino, A. / Buts, L. / Wyns, L. / Loris, R. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Interplay Between Metal Binding and cis/trans Isomerization in Legume Lectins: Structural and Thermodynamic Study of P. angolensis Lectin. Authors: Garcia-Pino, A. / Buts, L. / Wyns, L. / Loris, R. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gmp.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gmp.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/2gmp ftp://data.pdbj.org/pub/pdb/validation_reports/gm/2gmp | HTTPS FTP |
---|
-Related structure data
Related structure data | 2gmeC 2gmmC 2gn3C 2gn7C 2gnbC 2gndC 2gnmC 2gntC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | Subunits A and B together form the lectin dimer |
-Components
#1: Protein | Mass: 27558.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pterocarpus angolensis (plant) / Tissue: seed / References: UniProt: Q8GSD2 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.45 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 10% PEG6000, 20% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 373K, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 16471 / Num. obs: 16471 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.71 Å / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
| ||||||||||||||||||||
Refine LS restraints |
|