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Yorodumi- PDB-6t9a: Crystal structrue of RSL W31FW76F lectin mutant in complex with L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t9a | ||||||
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Title | Crystal structrue of RSL W31FW76F lectin mutant in complex with L-fucose | ||||||
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: 2 Å | ||||||
Authors | Houser, 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 | 6t9a.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t9a.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 6t9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t9a ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t9a | HTTPS FTP |
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-Related structure data
Related structure data | 6t99C 6t9bC 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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Unit cell |
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-Components
#1: Protein | Mass: 9655.491 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Double mutant W31F W76F / 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-FUC / #3: Sugar | ChemComp-FUL / #4: Chemical | #5: 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: 1.9 Å3/Da / Density % sol: 35.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 23% PEG 6000, 0.1M Glycine, 0.1M 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: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.15 Å / Num. all: 14315 / Num. obs: 14315 / % possible obs: 96.4 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.048 / Rrim(I) all: 0.071 / Rsym value: 0.053 / Net I/σ(I): 8.3 / Num. measured all: 28355 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.16 / Num. unique obs: 2071 / CC1/2: 0.933 / Rpim(I) all: 0.041 / Rrim(I) all: 0.063 / Rsym value: 0.047 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BT9 Resolution: 2→37.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.324 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.171 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: 57.58 Å2 / Biso mean: 23.392 Å2 / Biso min: 15.18 Å2
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Refinement step | Cycle: final / Resolution: 2→37.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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