+Open data
-Basic information
Entry | Database: PDB / ID: 7f9g | ||||||
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Title | Thrombocorticin in complex with Ca2+ and fucose | ||||||
Components | Thrombocorticin | ||||||
Keywords | SUGAR BINDING PROTEIN / bioactive protein / Thrombocorticin | ||||||
Function / homology | alpha-L-fucopyranose Function and homology information | ||||||
Biological species | Corticium sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.331 Å | ||||||
Authors | Kageyama, H. / Onodera, K. / Sakai, R. / Tanaka, Y. | ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation. Authors: Watari, H. / Kageyama, H. / Masubuchi, N. / Nakajima, H. / Onodera, K. / Focia, P.J. / Oshiro, T. / Matsui, T. / Kodera, Y. / Ogawa, T. / Yokoyama, T. / Hirayama, M. / Hori, K. / Freymann, D. ...Authors: Watari, H. / Kageyama, H. / Masubuchi, N. / Nakajima, H. / Onodera, K. / Focia, P.J. / Oshiro, T. / Matsui, T. / Kodera, Y. / Ogawa, T. / Yokoyama, T. / Hirayama, M. / Hori, K. / Freymann, D.M. / Imai, M. / Komatsu, N. / Araki, M. / Tanaka, Y. / Sakai, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f9g.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f9g.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 7f9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/7f9g ftp://data.pdbj.org/pub/pdb/validation_reports/f9/7f9g | HTTPS FTP |
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-Related structure data
Related structure data | 7f91C 7f9fSC 7f9jC 7fblC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14822.196 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corticium sp. (in: Fungi) (fungus) / Production host: Escherichia coli (E. coli) #2: Sugar | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.83 Å3/Da / Density % sol: 32.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: Sodium acetate, PEG 3350, PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→41.35 Å / Num. obs: 47092 / % possible obs: 99.8 % / Redundancy: 9.6 % / Rsym value: 0.057 / Net I/σ(I): 26.05 |
Reflection shell | Resolution: 1.33→1.41 Å / Num. unique obs: 7406 / Rsym value: 0.377 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7F9F Resolution: 1.331→30.428 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.331→30.428 Å
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Refine LS restraints |
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LS refinement shell |
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