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Yorodumi- PDB-2gn7: Metal-free (apo) P. angolensis seed lectin in complex with Man-al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gn7 | ||||||||||||
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Title | Metal-free (apo) P. angolensis seed lectin in complex with Man-alpha(1-3)Man-alpha(1-6)Man | ||||||||||||
Components | lectin | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / legume lectin / metal-free lectin / sugar complex / Man-alpha(1-3)Man-alpha(1-6)Man / beta sandwich | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pterocarpus angolensis (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gn7.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gn7.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gn7_validation.pdf.gz | 744.8 KB | Display | wwPDB validaton report |
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Full document | 2gn7_full_validation.pdf.gz | 769.7 KB | Display | |
Data in XML | 2gn7_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 2gn7_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/2gn7 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/2gn7 | HTTPS FTP |
-Related structure data
Related structure data | 2gmeC 2gmmC 2gmpC 2gn3C 2gnbC 2gndC 2gnmC 2gntC 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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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 | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-MAN / | #4: 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: 2.08 Å3/Da / Density % sol: 40.78 % |
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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 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2004 |
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: 2.9→15 Å / Num. all: 9174 / Num. obs: 9174 / % possible obs: 85.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.9→3 Å / % possible all: 71.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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