+Open data
-Basic information
Entry | Database: PDB / ID: 7e7t | ||||||
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Title | Crystal structure of RSL mutant in complex with sugar Ligand | ||||||
Components | Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein | ||||||
Keywords | SUGAR BINDING PROTEIN / Complex / Lectin / Fucose / Rhodamine | ||||||
Function / homology | Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / Chem-R2F / Fucose-binding lectin protein Function and homology information | ||||||
Biological species | Ralstonia solanacearum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Li, L. / Chen, G.S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of RSL mutant-R17A/R108A/R199A in complex with R2F Authors: Li, L. / Chen, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e7t.cif.gz | 225.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e7t.ent.gz | 182.2 KB | Display | PDB format |
PDBx/mmJSON format | 7e7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/7e7t ftp://data.pdbj.org/pub/pdb/validation_reports/e7/7e7t | HTTPS FTP |
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-Related structure data
Related structure data | 4csdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29091.568 Da / Num. of mol.: 2 / Mutation: R17A,R108A,R199A 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 BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1 #2: Chemical | ChemComp-R2F / #3: 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: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 277 K / Method: small tubes / pH: 7.5 Details: 20 mM Tris-HCl, 100 mM of NaCl; pH 7.5, Micro centrifuge tube sequentially put with RSL solution, pure b |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→67.74 Å / Num. obs: 32990 / % possible obs: 89.6 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Net I/σ(I): 9.2 / Num. measured all: 210690 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CSD Resolution: 1.98→67.74 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.19 / 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: 118.98 Å2 / Biso mean: 39.9042 Å2 / Biso min: 18.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→67.74 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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