+Open data
-Basic information
Entry | Database: PDB / ID: 6z5w | ||||||
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Title | The RSL - sulfonato-calix[8]arene complex, P213 form, MES pH 6.8 | ||||||
Components | Fucose-binding lectin protein | ||||||
Keywords | SUGAR BINDING PROTEIN / calixarene / protein framework / cage / crystal engineering / molecular glue / synthetic receptor / macrocycle / biomaterial | ||||||
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: 1.187 Å | ||||||
Authors | Engilberge, S. / Ramberg, K. / Crowley, P.B. | ||||||
Funding support | Ireland, 1items
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Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z5w.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z5w.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 6z5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/6z5w ftp://data.pdbj.org/pub/pdb/validation_reports/z5/6z5w | HTTPS FTP |
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-Related structure data
Related structure data | 6z5gC 6z5mC 6z5pC 6z5qC 6z5xC 6z5zC 6z60C 6z62C 7alfC 7algC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9733.562 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: Chemical | ChemComp-EVB / | ||||
#3: Chemical | ChemComp-SO4 / | ||||
#4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 35.6 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 6.8, 2.4 M Ammonium sulfate, 0.04 M sulfonato-calix[8]arene |
-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: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.187→45.132 Å / Num. obs: 28303 / % possible obs: 100 % / Redundancy: 36.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.021 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.187→1.207 Å / Redundancy: 19.7 % / Rmerge(I) obs: 1.427 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1395 / CC1/2: 0.794 / Rpim(I) all: 0.328 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BT9 Resolution: 1.187→45.132 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.51 / 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: 77.12 Å2 / Biso mean: 15.7184 Å2 / Biso min: 6.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.187→45.132 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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