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Yorodumi- PDB-6kbj: Structure of Lectin from Pleurotus ostreatus in complex with malonate -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kbj | ||||||
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Title | Structure of Lectin from Pleurotus ostreatus in complex with malonate | ||||||
Components | Lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / Lectin / Pleurotus ostreatus / Agglutinin / Ca binding / mushroom / fungi | ||||||
Function / homology | MALONATE ION / Lectin Function and homology information | ||||||
Biological species | Pleurotus ostreatus (oyster mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Vajravijayan, S. / Pletnev, S. / Luo, Z. / Gunasekaran, K. / Nandhagopal, N. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2020 Title: Crystallographic and calorimetric analysis on Pleurotus ostreatus lectin and its sugar complexes - promiscuous binding driven by geometry. Authors: Vajravijayan, S. / Pletnev, S. / Luo, Z. / Pletnev, V.Z. / Nandhagopal, N. / Gunasekaran, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kbj.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kbj.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/6kbj ftp://data.pdbj.org/pub/pdb/validation_reports/kb/6kbj | HTTPS FTP |
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-Related structure data
Related structure data | 6kbqC 6kc2C 6li7C 6likC 5w5nS 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: 39004.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pleurotus ostreatus (oyster mushroom) / References: UniProt: E7E2M2 | ||||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.29 Å3/Da / Density % sol: 80.44 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.9M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 15, 2017 / Details: 3.3 Undulator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→132 Å / Num. obs: 52573 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Χ2: 1.036 / Net I/σ(I): 7.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W5N Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.767 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.119 / 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: 132.86 Å2 / Biso mean: 34.541 Å2 / Biso min: 18.39 Å2
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Refinement step | Cycle: final / Resolution: 2.2→50 Å
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LS refinement shell | Resolution: 2.2→2.253 Å / Rfactor Rfree error: 0
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