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Yorodumi- PDB-2cyg: Crystal structure at 1.45- resolution of the major allergen endo-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cyg | ||||||
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Title | Crystal structure at 1.45- resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome | ||||||
Components | beta-1, 3-glucananse | ||||||
Keywords | HYDROLASE / endo-beta-1 / 3-glucanase / (beta-alpha)8-TIM-barrel / B-cell epitopes / allergen / banana | ||||||
Function / homology | Function and homology information glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Musa acuminata (dwarf banana) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Receveur-Brechot, V. / Czjzek, M. / Barre, A. / Roussel, A. / Peumans, W.J. / Van Damme, E.J.M. / Rouge, P. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal structure at 1.45-A resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome Authors: Receveur-Brechot, V. / Czjzek, M. / Barre, A. / Roussel, A. / Peumans, W.J. / Van Damme, E.J.M. / Rouge, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cyg.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cyg.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 2cyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/2cyg ftp://data.pdbj.org/pub/pdb/validation_reports/cy/2cyg | HTTPS FTP |
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-Related structure data
Related structure data | 1ghsS 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
#1: Protein | Mass: 33442.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Musa acuminata (dwarf banana) References: UniProt: O22317, glucan endo-1,3-beta-D-glucosidase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.034 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2002 |
Radiation | Monochromator: single wavelength / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→20 Å / Num. all: 53238 / Num. obs: 52014 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 10.46 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4819 / Rsym value: 0.129 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GHS Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.894 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.487 Å / Total num. of bins used: 20
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