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Yorodumi- PDB-1lu2: DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE BLOOD GROUP A T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lu2 | |||||||||
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Title | DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE BLOOD GROUP A TRISACCHARIDE | |||||||||
Components | LECTIN | |||||||||
Keywords | LECTIN / LEGUME LECTINS / DOLICHOS BIFLORUS SEED LECTIN / SUGAR BINDING | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Vigna unguiculata subsp. cylindrica (catjang) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 1lu2.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lu2.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lu2_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 1lu2_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 1lu2_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 1lu2_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/1lu2 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/1lu2 | HTTPS FTP |
-Related structure data
Related structure data | 1bjqC 1lu1C 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9999, 0.0016, 0.0136), Vector: |
-Components
#1: Protein | Mass: 27115.078 Da / Num. of mol.: 2 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 #2: Sugar | #3: Chemical | #4: Chemical | |
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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: 2.6 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.6 Details: 100 MM NACACO PH 6.6 15% (W/V) PEG-ME 5000 10 MM BLOOD GROUP A TRISACCHARIDE | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||
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: Jan 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. obs: 14331 / % possible obs: 85.2 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.1 / % possible all: 85.8 |
Reflection | *PLUS Num. measured all: 39403 |
Reflection shell | *PLUS Lowest resolution: 2.92 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FAT Resolution: 2.8→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED ONLY THE GALNAC RESIDUE OF THE BLOOD GROUP A TRISACCHARIDE IS VISIBLE IN THE ELECTRON DENSITY.
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Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.027 / 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: 0.289 |