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Yorodumi- PDB-6zum: Crystal structure of dimethylated RSL-N23H (RSL-B3) in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zum | ||||||||||||
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Title | Crystal structure of dimethylated RSL-N23H (RSL-B3) in complex with cucurbit[7]uril and zinc | ||||||||||||
Components | Fucose-binding lectin protein | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / cucurbituril / molecular glue / crystal engineering / dimethyllysine / zinc / b-propeller | ||||||||||||
Function / homology | Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / ACETATE ION / beta-D-fructopyranose / cucurbit[7]uril / Fucose-binding lectin protein Function and homology information | ||||||||||||
Biological species | Ralstonia solanacearum (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å | ||||||||||||
Authors | Guagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / Crowley, P.B. | ||||||||||||
Funding support | Ireland, 3items
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Citation | Journal: Cryst.Growth Des. / Year: 2020 Title: Metal-Mediated Protein-Cucurbituril Crystalline Architectures Authors: Guagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / 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 | 6zum.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zum.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/6zum ftp://data.pdbj.org/pub/pdb/validation_reports/zu/6zum | HTTPS FTP |
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-Related structure data
Related structure data | 6zukC 6zulC 6f7wS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 9866.798 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia solanacearum (bacteria) Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1 |
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#2: Sugar |
-Non-polymers , 5 types, 62 molecules
#3: Chemical | ChemComp-ACT / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-QQ7 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
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: 2.33 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% PEG 8000, 0.1 M TRIS-HCl pH 7.0, 0.2 M magnesium chloride |
-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: 0.98013 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98013 Å / Relative weight: 1 |
Reflection | Resolution: 1.589→34.159 Å / Num. obs: 13378 / % possible obs: 99.7 % / Redundancy: 9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.03 / Rrim(I) all: 0.096 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.589→1.617 Å / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 646 / CC1/2: 0.775 / Rpim(I) all: 0.332 / Rrim(I) all: 0.771 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F7W polyalanine Resolution: 1.589→34.159 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 25.75 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.71 Å2 / Biso mean: 43.2139 Å2 / Biso min: 16.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.589→34.159 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 6.809 Å / Origin y: 9.9386 Å / Origin z: 0.4441 Å
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Refinement TLS group |
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