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Yorodumi- PDB-6f7w: Crystal structure of dimethylated RSL - cucurbit[7]uril complex, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f7w | |||||||||
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Title | Crystal structure of dimethylated RSL - cucurbit[7]uril complex, C2221 Form | |||||||||
Components | Fucose-binding lectin protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / cucurbituril / dimethyllysine / supramolecular recognition | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Ralstonia solanacearum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å | |||||||||
Authors | Guagnini, F. / Rennie, M.L. / Crowley, P.B. | |||||||||
Funding support | Ireland, 1items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Authors: Guagnini, F. / Antonik, P.M. / Rennie, M.L. / O'Byrne, P. / Khan, A.R. / Pinalli, R. / Dalcanale, E. / 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 | 6f7w.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f7w.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 6f7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f7w_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6f7w_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6f7w_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 6f7w_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/6f7w ftp://data.pdbj.org/pub/pdb/validation_reports/f7/6f7w | HTTPS FTP |
-Related structure data
Related structure data | 6f7xC 6f7yC 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
#1: Protein | Mass: 9842.753 Da / Num. of mol.: 3 / Mutation: S88A Source method: isolated from a genetically manipulated source Details: Recombinant protein dimethylated at lysine residues and N-terminus Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: RSP795_21825, RSP799_05830, RUN39_v1_50103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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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: 2.76 Å3/Da / Density % sol: 55.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 200 mM Sodium Malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.28→43.6 Å / Num. obs: 78616 / % possible obs: 95 % / Redundancy: 4.5 % / CC1/2: 0.99 / Rpim(I) all: 0.022 / Rrim(I) all: 0.05 / Net I/σ(I): 18.8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bt9 chain A Resolution: 1.28→43.6 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.338 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0389 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.039 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.52 Å2 / Biso mean: 18.503 Å2 / Biso min: 9.59 Å2
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Refinement step | Cycle: final / Resolution: 1.28→43.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.28→1.313 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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