+Open data
-Basic information
Entry | Database: PDB / ID: 7fbl | ||||||
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Title | Thrombocorticin in complex with Ca2+ and mannose | ||||||
Components | Thrombocorticin | ||||||
Keywords | SUGAR BINDING PROTEIN / bioactive protein / thrombocorticin | ||||||
Function / homology | alpha-D-mannopyranose Function and homology information | ||||||
Biological species | Corticium sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.419 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 | 7fbl.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fbl.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 7fbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fbl_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7fbl_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7fbl_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 7fbl_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/7fbl ftp://data.pdbj.org/pub/pdb/validation_reports/fb/7fbl | HTTPS FTP |
-Related structure data
Related structure data | 7f91C 7f9fSC 7f9gC 7f9jC 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 | ChemComp-MAN / | #3: Chemical | #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: 1.86 Å3/Da / Density % sol: 33.75 % |
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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: 1.419→54.63 Å / Num. obs: 39544 / % possible obs: 99.7 % / Redundancy: 9.51 % / Rsym value: 0.082 / Net I/σ(I): 22.27 |
Reflection shell | Resolution: 1.419→1.5 Å / Num. unique obs: 6240 / Rsym value: 0.503 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7F9F Resolution: 1.419→33.082 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.53 / 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: 1.419→33.082 Å
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Refine LS restraints |
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LS refinement shell |
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