+Open data
-Basic information
Entry | Database: PDB / ID: 2phf | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Pterocarpus angolensis lectin complexed with Man-6 | ||||||||||||
Components | Lectin | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / lectin / carbohydrate / high mannose | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pterocarpus angolensis (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Garcia-Pino, A. / Buts, L. / Wyns, L. / Imberty, A. / Loris, R. | ||||||||||||
Citation | Journal: Plant Physiol. / Year: 2007 Title: How a plant lectin recognizes high mannose oligosaccharides Authors: Garcia-Pino, A. / Buts, L. / Wyns, L. / Imberty, A. / Loris, R. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2phf.cif.gz | 113.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2phf.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 2phf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2phf ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2phf | HTTPS FTP |
---|
-Related structure data
Related structure data | 2phrC 2phtC 2phuC 2phwC 2phxC 1q8pS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27558.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pterocarpus angolensis (plant) / References: UniProt: Q8GSD2 |
---|
-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose |
---|---|
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 235 molecules
#4: Chemical | #5: Chemical | #6: 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: 53.28 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 100 mM cacolylate pH 6.6, 200 mM CaCl2, 18% PEG-6000, 20 mM Man(a1-3)Man, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. all: 34604 / Num. obs: 34604 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3538 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Q8P Resolution: 2.1→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
| ||||||||||||||||||||
Refine LS restraints |
|