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Yorodumi- PDB-5ida: Crystal structure of CGL1 from Crassostrea gigas, mannose-bound f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ida | ||||||
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Title | Crystal structure of CGL1 from Crassostrea gigas, mannose-bound form (CGL1/MAN) | ||||||
Components | Natterin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / CGL1 / lectin / Crassostrea gigas / N-type / mannose | ||||||
Function / homology | DM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / beta-D-mannopyranose / Natterin-3 Function and homology information | ||||||
Biological species | Crassostrea gigas (Pacific oyster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å | ||||||
Authors | Unno, H. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Mannose-Specific Lectin CGL1 from the Pacific Oyster Crassostrea gigas. Authors: Unno, H. / Matsuyama, K. / Tsuji, Y. / Goda, S. / Hiemori, K. / Tateno, H. / Hirabayashi, J. / Hatakeyama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ida.cif.gz | 255.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ida.ent.gz | 209.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ida.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ida_validation.pdf.gz | 336.2 KB | Display | wwPDB validaton report |
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Full document | 5ida_full_validation.pdf.gz | 344.7 KB | Display | |
Data in XML | 5ida_validation.xml.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/5ida ftp://data.pdbj.org/pub/pdb/validation_reports/id/5ida | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15578.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Crassostrea gigas (Pacific oyster) / References: UniProt: K1QRB6 #2: Sugar | #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: 2.03 Å3/Da / Density % sol: 39.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 160510 / % possible obs: 79.6 % / Redundancy: 3.9 % / Net I/σ(I): 17 |
-Processing
Software |
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Refinement | Resolution: 1.1→17.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.505 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.846 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→17.87 Å
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Refine LS restraints |
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