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Yorodumi- PDB-4agg: Structure of a tetrameric galectin from Cinachyrella sp. (Ball sponge) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4agg | ||||||
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Title | Structure of a tetrameric galectin from Cinachyrella sp. (Ball sponge) | ||||||
Components | GALECTIN | ||||||
Keywords | CARBOHYDRATE-BINDING PROTEIN / GALECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CINACHYRELLA SP. (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Freymann, D.M. / Focia, P.J. / Sakai, R. / Swanson, G.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structure of a Tetrameric Galectin from Cinachyrella Sp. (Ball Sponge). Authors: Freymann, D.M. / Nakamura, Y. / Focia, P.J. / Sakai, R. / Swanson, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4agg.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4agg.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 4agg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4agg_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 4agg_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 4agg_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 4agg_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/4agg ftp://data.pdbj.org/pub/pdb/validation_reports/ag/4agg | HTTPS FTP |
-Related structure data
Related structure data | 4agrC 4agvC 1is5S 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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Unit cell |
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-Components
#1: Protein | Mass: 16074.089 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) CINACHYRELLA SP. (invertebrata) / References: UniProt: I0IV54*PLUS #2: Chemical | ChemComp-CL / | #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: 2.43 Å3/Da / Density % sol: 49.5 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5, 30% PEG3000 |
-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→49.75 Å / Num. obs: 6308 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.98→3.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 74.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IS5, SIDECHAINS TRUNCATED Resolution: 2.98→40.22 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.854 / SU B: 24.079 / SU ML: 0.424 / Cross valid method: THROUGHOUT / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY TORSION ANGLE OUTLIERS IN THE STRUCTURE OCCUR FOR SOME RESIDUES IN POORLY DEFINED SURFACE LOOPS.
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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: 55.097 Å2
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Refinement step | Cycle: LAST / Resolution: 2.98→40.22 Å
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Refine LS restraints |
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