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Yorodumi- PDB-6jms: CJP38, a beta-1,3-glucanase and allergen of Cryptomeria japonica ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jms | ||||||
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Title | CJP38, a beta-1,3-glucanase and allergen of Cryptomeria japonica pollen | ||||||
Components | Pollen allergen CJP38 | ||||||
Keywords | HYDROLASE / Beta-1 / 3-glucanase / Allergen / Tim barrel | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Cryptomeria japonica (Japanese cedar) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Takashima, T. / Numata, T. / Fukamizo, T. / Ohnuma, T. | ||||||
Citation | Journal: To Be Published Title: CJP38, a beta-1,3-glucanase and allergen of Cryptomeria japonica pollen Authors: Takashima, T. / Fukamizo, T. / Ohnuma, T. / Numata, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jms.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jms.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jms_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
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Full document | 6jms_full_validation.pdf.gz | 426.1 KB | Display | |
Data in XML | 6jms_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 6jms_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/6jms ftp://data.pdbj.org/pub/pdb/validation_reports/jm/6jms | HTTPS FTP |
-Related structure data
Related structure data | 2cygS 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: 35773.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptomeria japonica (Japanese cedar) / Production host: Escherichia coli (E. coli) References: UniProt: Q588B8, glucan endo-1,3-beta-D-glucosidase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M calcium chloride, 20% Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 50705 / % possible obs: 99.4 % / Redundancy: 13.3 % / Rpim(I) all: 0.016 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 2499 / CC1/2: 0.958 / Rpim(I) all: 0.116 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CYG Resolution: 1.5→35.711 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.944 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063 / 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: 18.541 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→35.711 Å
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Refine LS restraints |
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