+Open data
-Basic information
Entry | Database: PDB / ID: 6a7t | |||||||||||||||
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Title | Ca2+-independent C-type lectin SPL-1 from Saxidomus purpuratus | |||||||||||||||
Components | (N-acetylglucosamine-specific lectin) x 2 | |||||||||||||||
Keywords | SUGAR BINDING PROTEIN / SPL-1 / lectin / bivalve / Saxidomus purpuratus / C-type | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Saxidomus purpuratus (invertebrata) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | |||||||||||||||
Authors | Unno, H. / Hatakeyama, T. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Protein Sci. / Year: 2019 Title: Novel Ca2+-independent carbohydrate recognition of the C-type lectins, SPL-1 and SPL-2, from the bivalve Saxidomus purpuratus. Authors: Unno, H. / Itakura, S. / Higuchi, S. / Goda, S. / Yamaguchi, K. / Hatakeyama, T. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a7t.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a7t.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 6a7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a7t_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 6a7t_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 6a7t_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 6a7t_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/6a7t ftp://data.pdbj.org/pub/pdb/validation_reports/a7/6a7t | HTTPS FTP |
-Related 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: 17981.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saxidomus purpuratus (invertebrata) / References: UniProt: A0A2Z6G7U6 | ||
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#2: Protein | Mass: 17898.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saxidomus purpuratus (invertebrata) / References: UniProt: A0A2Z6G7U3 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: 30% PEG3000, 100mM CHES/NaOH (pH 9.5) |
-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: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 37306 / % possible obs: 99.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.616 |
-Processing
Software |
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Refinement | Resolution: 1.6→38.21 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.001 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.101 / 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: 16.811 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→38.21 Å
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Refine LS restraints |
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