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Yorodumi- PDB-2gnt: EDTA treated P. angolensis lectin (PAL) remetallized with calcium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gnt | |||||||||
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Title | EDTA treated P. angolensis lectin (PAL) remetallized with calcium (1 hour treatment) | |||||||||
Components | lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / legume lectin / remetallization / PAL / metal binding / beta sandwich | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pterocarpus angolensis (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 | 2gnt.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gnt.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/2gnt ftp://data.pdbj.org/pub/pdb/validation_reports/gn/2gnt | HTTPS FTP |
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-Related structure data
Related structure data | 2gmeC 2gmmC 2gmpC 2gn3C 2gn7C 2gnbC 2gndC 2gnmC 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: Chemical | ChemComp-CA / #3: 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: 2.69 Å3/Da / Density % sol: 54.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG8000, 0.2M calcium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 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: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→25 Å / Num. all: 39724 / Num. obs: 39724 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.02→2.07 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.02→25 Å
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Refine LS restraints |
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