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Yorodumi- PDB-6t9b: Crystal structrue of RSL W31A lectin mutant in complex with alpha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t9b | ||||||
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Title | Crystal structrue of RSL W31A lectin mutant in complex with alpha-methylfucoside | ||||||
Components | Fucose-binding lectin protein | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / beta-propeller / fucose-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ralstonia solanacearum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Houser, J. / Komarek, J. / Kozmon, S. / Wimmerova, M. | ||||||
Citation | Journal: Chemistry / Year: 2020 Title: The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. Authors: Houser, J. / Kozmon, S. / Mishra, D. / Hammerova, Z. / Wimmerova, M. / Koca, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t9b.cif.gz | 189.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t9b.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 6t9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t9b ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t9b | HTTPS FTP |
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-Related structure data
Related structure data | 6t99C 6t9aC 2bt9S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 9618.430 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Details: Mutant W31A / Source: (gene. exp.) Ralstonia solanacearum (bacteria) Gene: RSP795_21825, RSP799_05830, RSP822_19650, RUN39_v1_50103 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1 #2: Sugar | ChemComp-MFU / #3: Chemical | ChemComp-GLY / #4: Water | ChemComp-HOH / | 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: 1.91 Å3/Da / Density % sol: 35.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 26% PEG6K, 0.1M glycine, 0.1 M Tris/HCl pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→38.27 Å / Num. all: 112322 / Num. obs: 112322 / % possible obs: 95.6 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.034 / Rrim(I) all: 0.048 / Rsym value: 0.034 / Net I/σ(I): 10.9 / Num. measured all: 197944 |
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.183 / Num. unique obs: 15776 / Rpim(I) all: 0.016 / Rrim(I) all: 0.023 / Rsym value: 0.016 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BT9 Resolution: 1.46→38.15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.039 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.15 Å2 / Biso mean: 11.129 Å2 / Biso min: 6.37 Å2
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Refinement step | Cycle: final / Resolution: 1.46→38.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.498 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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