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Yorodumi- PDB-5krp: Frutapin, a lectin from Artocarpus incisa: Cloning, Expressing an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5krp | ||||||
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Title | Frutapin, a lectin from Artocarpus incisa: Cloning, Expressing and Structural Analysis. | ||||||
Components | Frutapin | ||||||
Keywords | Carbohydrate Binding Protein / Protein / Lectin / ApoFrutapin / Artocarpus altillis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Artocarpus altilis (breadfruit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | de Sousa, F.D. / Coker, A.R. / Guan, Y. / Guo, J. / de Oliveira Monteiro-Moreira, A.C. / de Azevedo Moreira, R. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Biosci. Rep. / Year: 2017 Title: Frutapin, a lectin fromArtocarpus incisa(breadfruit): cloning, expression and molecular insights. Authors: de Sousa, F.D. / da Silva, B.B. / Furtado, G.P. / Carneiro, I.S. / Lobo, M.D.P. / Guan, Y. / Guo, J. / Coker, A.R. / Lourenzoni, M.R. / Guedes, M.I.F. / Owen, J.S. / Abraham, D.J. / Monteiro- ...Authors: de Sousa, F.D. / da Silva, B.B. / Furtado, G.P. / Carneiro, I.S. / Lobo, M.D.P. / Guan, Y. / Guo, J. / Coker, A.R. / Lourenzoni, M.R. / Guedes, M.I.F. / Owen, J.S. / Abraham, D.J. / Monteiro-Moreira, A.C.O. / Moreira, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5krp.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5krp.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 5krp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/5krp ftp://data.pdbj.org/pub/pdb/validation_reports/kr/5krp | HTTPS FTP |
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-Related structure data
Related structure data | 5m6oC 5tqzC 4akdS 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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Unit cell |
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-Components
#1: Protein | Mass: 16292.272 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Artocarpus altilis (breadfruit) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2D0TC52*PLUS #2: Chemical | ChemComp-GOL / #3: 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: 2.37 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Potassium phosphate monobasic, PEG 8000, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→47.77 Å / Num. obs: 85305 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.58→1.62 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 8.6 / CC1/2: 1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AKD Resolution: 1.58→38.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.245 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 23.793 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→38.48 Å
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Refine LS restraints |
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