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Yorodumi- PDB-6vb8: Crystal structure of a lectin from Canavalia brasiliensis seed (C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vb8 | ||||||
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Title | Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with indole-3-acetic acid | ||||||
Components | Concanavalin-Br | ||||||
Keywords | SUGAR BINDING PROTEIN / Canavalia brasiliensis / ConBr / IAA / indole-3-acetic acid / auxin / Lectin / ABU / alpha-aminobutyric acid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Canavalia brasiliensis (Brazilian jackbean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bezerra, E.H.S. / Queiroz, P.P. / da Silva, F.M.S. / Girao, M.S. / Sales, M.V. / Paiva, C.P.S. / Freire, V.N. / Rocha, B.A.M. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Structural insights into phytohormone interaction to plant lectin ConBr Authors: Bezerra, E.H.S. / Sales, M.V. / Girao, M.S. / da Silva, F.M.S. / Queiroz, P.P. / Paiva, C.P.S. / Freire, V.N. / Rocha, B.A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vb8.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vb8.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 6vb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vb8_validation.pdf.gz | 781.6 KB | Display | wwPDB validaton report |
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Full document | 6vb8_full_validation.pdf.gz | 782.5 KB | Display | |
Data in XML | 6vb8_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 6vb8_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/6vb8 ftp://data.pdbj.org/pub/pdb/validation_reports/vb/6vb8 | HTTPS FTP |
-Related structure data
Related structure data | 3ju9S 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25592.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Canavalia brasiliensis (Brazilian jackbean) References: UniProt: P55915 |
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-Non-polymers , 7 types, 51 molecules
#2: Chemical | ChemComp-GOL / | ||||||
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#3: Chemical | ChemComp-CA / | ||||||
#4: Chemical | ChemComp-MN / | ||||||
#5: Chemical | #6: Chemical | ChemComp-DBB / | #7: Chemical | ChemComp-IAC / | #8: Water | ChemComp-HOH / | |
-Details
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: 2.39 Å3/Da / Density % sol: 48.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.458 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.69 Å / Num. obs: 12527 / % possible obs: 98.3 % / Redundancy: 11.9 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 1596 / CC1/2: 0.994 / Rpim(I) all: 0.073 / Rrim(I) all: 0.225 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3JU9 Resolution: 2.2→49.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.134 / SU ML: 0.159 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.21 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.67 Å2 / Biso mean: 45.966 Å2 / Biso min: 28.47 Å2
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Refinement step | Cycle: final / Resolution: 2.2→49.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 14.386 Å / Origin y: 14.256 Å / Origin z: 10.956 Å
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