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Yorodumi- PDB-1q8q: Pterocarpus angolensis lectin (PAL) in complex with the dimannosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q8q | ||||||||||||
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Title | Pterocarpus angolensis lectin (PAL) in complex with the dimannoside Man(alpha1-4)Man | ||||||||||||
Components | lectin | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / lectin / carbohydrate / mannose | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pterocarpus angolensis (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||||||||
Authors | Loris, R. / Van Walle, I. / De Greve, H. / Beeckmans, S. / Deboeck, F. / Wyns, L. / Bouckaert, J. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural Basis of Oligomannose Recognition by the Pterocarpus angolensis Seed Lectin Authors: Loris, R. / Van Walle, I. / De Greve, H. / Beeckmans, S. / Deboeck, F. / Wyns, L. / Bouckaert, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q8q.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q8q.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 1q8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q8q ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q8q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27558.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pterocarpus angolensis (plant) / References: GenBank: 27368665, UniProt: Q8GSD2*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | #5: 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: 53.02 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, Ca-acetate, Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.45 / Method: vapor diffusion, hanging drop / Details: Loris, R., (2003) J.BIOL.CHEM., 278, 16297. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→35 Å / Num. all: 36449 / Num. obs: 36449 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.39 / Num. unique all: 3544 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 209488 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.9 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.05→19.9 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.2179 / Rfactor Rwork: 0.1841 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |