[English] 日本語
Yorodumi- PDB-8q6b: The RSL-D32N - sulfonato-calix[8]arene complex, I23 form, citrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q6b | ||||||
---|---|---|---|---|---|---|---|
Title | The RSL-D32N - sulfonato-calix[8]arene complex, I23 form, citrate pH 4.0, obtained by cross-seeding | ||||||
Components | Fucose-binding lectin protein | ||||||
Keywords | SUGAR BINDING PROTEIN / biomaterials / beta-propeller / crystal engineering / molecular glue | ||||||
Function / homology | Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / beta-D-fructopyranose / 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: 1.52 Å | ||||||
Authors | Flood, R.J. / Crowley, P.B. | ||||||
Funding support | Ireland, 1items
| ||||||
Citation | Journal: Cryst.Growth Des. / Year: 2024 Title: Supramolecular Synthons in Protein-Ligand Frameworks. Authors: Flood, R.J. / Mockler, N.M. / Thureau, A. / Malinska, M. / Crowley, P.B. #1: Journal: J Am Chem Soc / Year: 2021 Title: Facile Fabrication of Protein-Macrocycle Frameworks. Authors: Ramberg, K.O. / Engilberge, S. / Skorek, T. / Crowley, P.B. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8q6b.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8q6b.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 8q6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/8q6b ftp://data.pdbj.org/pub/pdb/validation_reports/q6/8q6b | HTTPS FTP |
---|
-Related structure data
Related structure data | 8q6aC 8q6cC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 9732.577 Da / Num. of mol.: 1 / Mutation: D32N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia solanacearum (bacteria) Gene: E7Z57_08365, HF909_06975, HXP36_18875, RSP795_21825, RSP822_19650, RUN39_v1_50103 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.32 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 100 mM tri-Sodium citrate pH 4.0, 1000 mM Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2022 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→45.79 Å / Num. obs: 36271 / % possible obs: 100 % / Redundancy: 34.4 % / Biso Wilson estimate: 18.66 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.117 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.52→1.55 Å / Num. unique obs: 1805 / CC1/2: 0.748 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→39.65 Å / SU ML: 0.1251 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.038 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→39.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|