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Yorodumi- PDB-5b4s: Crystal Structure of GH80 chitosanase from Mitsuaria chitosanitabida -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b4s | ||||||
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Title | Crystal Structure of GH80 chitosanase from Mitsuaria chitosanitabida | ||||||
Components | Chitosanase | ||||||
Keywords | HYDROLASE / CHITOSANASE / GLYCOSIDE HYDROLASE / CHITOSAN | ||||||
Function / homology | Function and homology information chitosanase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Mitsuaria chitosanitabida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Kumasaka, T. / Yorinaga, Y. / Yamamoto, M. / Hamada, K. / Kawamukai, M. | ||||||
Citation | Journal: FEBS Lett. / Year: 2017 Title: Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida Authors: Yorinaga, Y. / Kumasaka, T. / Yamamoto, M. / Hamada, K. / Kawamukai, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b4s.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b4s.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 5b4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/5b4s ftp://data.pdbj.org/pub/pdb/validation_reports/b4/5b4s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35685.641 Da / Num. of mol.: 2 / Fragment: UNP residues 81-391 / Mutation: T128V Source method: isolated from a genetically manipulated source Details: Expression tag "MRGSHHHHHHTDPH" was attached to the N-terminus of the mature protein. Since the UniProt O82856 entry includes pre-pro sequence (1-80), the mature protein starts at 81th Ala residue. Source: (gene. exp.) Mitsuaria chitosanitabida (bacteria) / Gene: choA / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: O82856 #2: 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: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, ammonium sulphate, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 8, 2001 |
Radiation | Monochromator: Diamond (400) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→43.66 Å / Num. obs: 61905 / % possible obs: 99.26 % / Redundancy: 7.2 % / Biso Wilson estimate: 14.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.74 |
Reflection shell | Resolution: 1.75→1.812 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 12.38 / % possible all: 98.65 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→43.659 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→43.659 Å
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Refine LS restraints |
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LS refinement shell |
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