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Yorodumi- PDB-5ava: Crystal structure of PHA-E lectin in complex with bisected glycan -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ava | |||||||||
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Title | Crystal structure of PHA-E lectin in complex with bisected glycan | |||||||||
Components | Erythroagglutinin | |||||||||
Keywords | SUGAR BINDING PROTEIN / lectin / glycan | |||||||||
Function / homology | Function and homology information mannose binding / defense response / toxin activity / carbohydrate binding Similarity search - Function | |||||||||
Biological species | Phaseolus vulgaris (French bean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Nagae, M. / Yamaguchi, Y. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins Authors: Nagae, M. / Kanagawa, M. / Morita-Matsumoto, K. / Hanashima, S. / Kizuka, Y. / Taniguchi, N. / Yamaguchi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ava.cif.gz | 390.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ava.ent.gz | 319.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ava.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/5ava ftp://data.pdbj.org/pub/pdb/validation_reports/av/5ava | HTTPS FTP |
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-Related structure data
Related structure data | 5av7C 3wcsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29818.379 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: V5YN37, UniProt: P05088*PLUS #2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #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: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1M sodium acetate (pH 4.5), 25 %(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. obs: 45064 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rsym value: 0.071 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WCS Resolution: 3→100 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.842 / SU B: 21.191 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.503 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.106 Å2
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Refinement step | Cycle: 1 / Resolution: 3→100 Å
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Refine LS restraints |
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