+Open data
-Basic information
Entry | Database: PDB / ID: 5t50 | ||||||
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Title | LIGAND-FREE LECTIN FROM BAUHINIA FORFICATA | ||||||
Components | Lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / LEGUME LECTIN / CONCANAVALIN A / GALNAC-SPECIFIC / LIGAND-FREE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bauhinia forficata (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Lubkowski, J. / Wlodawer, A. | ||||||
Citation | Journal: FEBS J. / Year: 2017 Title: Structural analysis and unique molecular recognition properties of a Bauhinia forficata lectin that inhibits cancer cell growth. Authors: Lubkowski, J. / Durbin, S.V. / Silva, M.C. / Farnsworth, D. / Gildersleeve, J.C. / Oliva, M.L. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t50.cif.gz | 216.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t50.ent.gz | 171.7 KB | Display | PDB format |
PDBx/mmJSON format | 5t50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t50_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 5t50_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 5t50_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5t50_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/5t50 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/5t50 | HTTPS FTP |
-Related structure data
Related structure data | 5t52C 5t54C 5t55C 5t5jC 5t5lC 5t5oC 5t5pC 1hqlS 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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Details | DIMER AS DETERMINED BY ANALYTICAL ULTRACENTRIFUGATION |
-Components
#1: Protein | Mass: 27143.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bauhinia forficata (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P86993 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EDO / #4: 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: 2.49 Å3/Da / Density % sol: 50.58 % / Description: BLOCKS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PROTEIN CONCENTRATION 5-8 MG/ML IN 0.05 M HEPES BUFFER (pH 7.5) AND 0.15 M NACL, PRECIPITANT: 12% (W/W) PEG8000, 8% (W/V) ETHYLENE GLYCOL, 0.1 M HEPES (pH 7.5), DROPLETS RATIO: 1:1 PH range: 7 - 8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Sep 5, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.43→50 Å / Num. obs: 90961 / % possible obs: 95.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.059 / Net I/av σ(I): 23.179 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HQL Resolution: 1.43→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.691 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / 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: 108.81 Å2 / Biso mean: 17.109 Å2 / Biso min: 7.62 Å2
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Refinement step | Cycle: final / Resolution: 1.43→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.428→1.465 Å / Total num. of bins used: 20
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