+Open data
-Basic information
Entry | Database: PDB / ID: 6sth | ||||||
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Title | Highly cationic RSL-R8 in complex with sulfonato-calix[8]arene | ||||||
Components | Fucose-binding lectin protein | ||||||
Keywords | SUGAR BINDING PROTEIN / Molecular Glue / Calixarene / Supramolecular interactions / Sulfonato-calix[8]arene / ligand conformation | ||||||
Function / homology | Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / sulfonato-calix[8]arene / Fucose-binding lectin protein Function and homology information | ||||||
Biological species | Ralstonia solanacearum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.726 Å | ||||||
Authors | Skorek, T. / Engilberge, S. / Crowley, P.B. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: To Be Published Title: Highly cationic RSL-R8 in complex with sulfonato-calix[8]arene Authors: Skorek, T. / Engilberge, S. / Crowley, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sth.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sth.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/6sth ftp://data.pdbj.org/pub/pdb/validation_reports/st/6sth | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9887.790 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia solanacearum (bacteria) Gene: RSP795_21825, RSP799_05830, RSP822_19650, RUN39_v1_50103 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | #5: 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: 3.18 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.6 mM RSL-R8 combined 33 mM sulfonato-calix[8]arene were crystallized using 0.1 M TRIS; pH 8.5, 1.26 M Ammonium sulfate, 0.2M Lithium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→59.3 Å / Num. obs: 25591 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 19.93 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.192 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.73→1.76 Å / Num. unique obs: 1242 / Rpim(I) all: 0.055 / Rrim(I) all: 1.691 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.726→39.302 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 29.28 / 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: 1.726→39.302 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 43.1291 Å / Origin y: 33.2013 Å / Origin z: 57.378 Å
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Refinement TLS group | Selection details: all |