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Yorodumi- PDB-5av7: Crystal structure of Calsepa lectin in complex with bisected glycan -
+Open data
-Basic information
Entry | Database: PDB / ID: 5av7 | |||||||||
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Title | Crystal structure of Calsepa lectin in complex with bisected glycan | |||||||||
Components | Lectin | |||||||||
Keywords | SUGAR BINDING PROTEIN / Lectin / glycan | |||||||||
Function / homology | Function and homology information D-glucose binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / D-mannose binding / cell adhesion molecule binding / positive regulation of mitotic nuclear division / carbohydrate binding / protein homodimerization activity / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Calystegia sepium (hedge bindweed) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 5av7.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5av7.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 5av7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5av7_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5av7_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5av7_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 5av7_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/5av7 ftp://data.pdbj.org/pub/pdb/validation_reports/av/5av7 | HTTPS FTP |
-Related structure data
Related structure data | 5avaC 1ouwS 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: 15872.536 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Calystegia sepium (hedge bindweed) / Production host: Escherichia coli (E. coli) / References: UniProt: P93114 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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: 2.18 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes-Na (pH 7.5), 3.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100 Å / Num. obs: 44270 / % possible obs: 97 % / Redundancy: 1.9 % / Rsym value: 0.088 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.9 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OUW Resolution: 1.85→54.77 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.307 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.178 / 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: 23.096 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→54.77 Å
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Refine LS restraints |
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