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Yorodumi- PDB-7pr5: Cocrystal of an RSL-N23H and sulfonato-thiacalix[4]arene - zinc c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pr5 | ||||||||||||
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Title | Cocrystal of an RSL-N23H and sulfonato-thiacalix[4]arene - zinc complex | ||||||||||||
Components | Fucose-binding lectin protein | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / calixarene / molecular glue / metal binding / synthetic receptor / b-propeller / thiacalixarene | ||||||||||||
Function / homology | Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / sulfonato-thiacalix[4]arene / beta-D-fructopyranose / Fucose-binding lectin protein Function and homology information | ||||||||||||
Biological species | Ralstonia solanacearum (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||||||||
Authors | Flood, R.J. / Ramberg, K. / Guagnini, F. / Crowley, P.B. | ||||||||||||
Funding support | Ireland, 3items
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Citation | Journal: Cryst.Growth Des. / Year: 2022 Title: Protein Frameworks with Thiacalixarene and Zinc. Authors: Flood, R.J. / Ramberg, K.O. / Mengel, D.B. / Guagnini, F. / 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 | 7pr5.cif.gz | 241.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pr5.ent.gz | 194.3 KB | Display | PDB format |
PDBx/mmJSON format | 7pr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/7pr5 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/7pr5 | HTTPS FTP |
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-Related structure data
Related structure data | 7pr2C 7pr3C 7pr4C 2bt9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 35 molecules ABCDEFGHIJKL
#1: Protein | Mass: 9757.606 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia solanacearum (bacteria) Gene: E7Z57_08365, HXP36_18875, RSP795_21825, RSP822_19650, RUN39_v1_50103 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1 #2: Sugar | ChemComp-BDF / |
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-Non-polymers , 4 types, 867 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-80M / | #6: Water | ChemComp-HOH / | |
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-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: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 16% PEG 3350, 200 mM tri-Sodium citrate pH 8.3, 60 mM zinc acetate |
-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: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→46.84 Å / Num. obs: 85149 / % possible obs: 99.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 32.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.036 / Rrim(I) all: 0.132 / Net I/σ(I): 14.8 / Num. measured all: 1155816 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BT9 Resolution: 1.94→46.84 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.99 / 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: 76.6 Å2 / Biso mean: 33.5422 Å2 / Biso min: 17.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→46.84 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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