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Yorodumi- PDB-6gl5: Crystal Structure of dimethylated RSL - sulfonatocalix[4]arene complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gl5 | |||||||||
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Title | Crystal Structure of dimethylated RSL - sulfonatocalix[4]arene complex | |||||||||
Components | Fucose-binding lectin protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / calixarene / dimethyllysine / supramolecular recognition | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Ralstonia solanacearum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Guagnini, F. / Rennie, M.L. / Crowley, P.B. | |||||||||
Funding support | Ireland, 1items
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Citation | Journal: To Be Published Title: Protein Crystallization via Sulfonatocalix[4]arene Dimethylammonium Complexation Authors: Guagnini, F. / Antonik, P.M. / Rennie, M.L. / 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 | 6gl5.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gl5.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/6gl5 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/6gl5 | HTTPS FTP |
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-Related structure data
Related structure data | 2bt9S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 2 - 90 / Label seq-ID: 2 - 90
NCS ensembles :
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-Components
-Protein , 1 types, 3 molecules ABC
#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: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1 |
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-Non-polymers , 7 types, 394 molecules
#2: Chemical | ChemComp-T3Y / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-SO4 / | #8: 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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.8 M ammonium sulfate, 0.1 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | |||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 3, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.6→45.94 Å / Num. obs: 42850 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.1 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BT9 chain A Resolution: 1.6→38.02 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.314 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.08 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: 67.52 Å2 / Biso mean: 17.219 Å2 / Biso min: 7.66 Å2
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Refinement step | Cycle: final / Resolution: 1.6→38.02 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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