+Open data
-Basic information
Entry | Database: PDB / ID: 2phr | ||||||||||||
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Title | Pterocarpus angolensis lectin (PAL) in complex with Man-7D1 | ||||||||||||
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 / MOELECULAR REPLACEMENT / Resolution: 1.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2phr.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2phr.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 2phr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2phr ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2phr | HTTPS FTP |
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-Related structure data
Related structure data | 2phfC 2phtC 2phuC 2phwC 2phxC 1q8pS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose |
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#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, 240 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 100 mM Cacodylate pH 6.6, 200 mM CaCl2, 18% (w/v) PEG-6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. all: 46128 / Num. obs: 46128 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 4.23 / Num. unique all: 4537 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOELECULAR REPLACEMENT Starting model: PDB entry 1Q8P Resolution: 1.9→15 Å / Cross valid method: thoughout / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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