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Yorodumi- PDB-1lu1: THE STRUCTURE OF THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lu1 | |||||||||
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Title | THE STRUCTURE OF THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE FORSSMAN DISACCHARIDE | |||||||||
Components | LECTIN | |||||||||
Keywords | LECTIN / LEGUME LECTINS / FORSSMAN DISACCHARIDE / DOLICHOS BIFLORUS SEED LECTIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Vigna unguiculata subsp. cylindrica (catjang) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Hamelryck, T.W. / Loris, R. / Bouckaert, J. / Strecker, G. / Imberty, A. / Fernandez, E. / Wyns, L. / Etzler, M.E. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus. Authors: Hamelryck, T.W. / Loris, R. / Bouckaert, J. / Dao-Thi, M.H. / Strecker, G. / Imberty, A. / Fernandez, E. / Wyns, L. / Etzler, M.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lu1.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lu1.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/1lu1 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/1lu1 | HTTPS FTP |
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-Related structure data
Related structure data | 1bjqC 1lu2C 1lulC 1fatS 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
#1: Protein | Mass: 27115.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DOLICHOS BIFLORUS SEED LECTIN Source: (gene. exp.) Vigna unguiculata subsp. cylindrica (catjang) Species: Vigna unguiculata / Strain: subsp. cylindrica / Organ: SEED / Production host: Escherichia coli (E. coli) / References: UniProt: P05045 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose / Forssman antigen fragment |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-ADE / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 100 MM HEPES PH 7.5 0.2 M MGCL2 30% (W/V) PEG 400 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 13175 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.6→2.62 Å / Redundancy: 7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.27 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 91892 / Rmerge(I) obs: 0.146 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FAT Resolution: 2.6→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.355 |