+Open data
-Basic information
Entry | Database: PDB / ID: 1n3p | |||||||||
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Title | Pterocarpus angolensis lectin in complex with sucrose | |||||||||
Components | lectin PAL | |||||||||
Keywords | SUGAR BINDING PROTEIN / lectin / carbohydrate recognition / sucrose | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pterocarpus angolensis (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Loris, R. / Imberty, A. / Beeckmans, S. / Van Driessche, E. / Read, J.S. / Bouckaert, J. / De Greve, H. / Buts, L. / Wyns, L. | |||||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Crystal structure of Pterocarpus angolensis lectin in complex with glucose, sucrose, and turanose Authors: Loris, R. / Imberty, A. / Beeckmans, S. / Van Driessche, E. / Read, J.S. / Bouckaert, J. / De Greve, H. / Buts, L. / Wyns, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n3p.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n3p.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 1n3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n3p_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1n3p_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1n3p_validation.xml.gz | 21 KB | Display | |
Data in CIF | 1n3p_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n3p ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n3p | HTTPS FTP |
-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: 27575.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pterocarpus angolensis (plant) / References: UniProt: Q8GSD2 #2: Polysaccharide | #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: 53.05 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG-8000, Na-cacodylate, Ca-acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.45 | ||||||||||||||||||||||||||||||||||||||||||
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: BW7B / Wavelength: 0.84 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 24, 2001 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. all: 34823 / Num. obs: 34823 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.31 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.99 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.477 / Num. unique all: 3394 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 5 Å / Num. measured all: 115196 |
Reflection shell | *PLUS % possible obs: 99.2 % / Num. unique obs: 3394 / Num. measured obs: 11024 / Mean I/σ(I) obs: 3.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refinement | *PLUS Lowest resolution: 5 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.178 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.24 |