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Yorodumi- PDB-8jjm: X-ray crystal structure of a multifunctional enzyme (Amy63) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jjm | |||||||||
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Title | X-ray crystal structure of a multifunctional enzyme (Amy63) from Vibrio alginolyticus 63 | |||||||||
Components | Amy63 | |||||||||
Keywords | HYDROLASE / amylase | |||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / calcium ion binding Similarity search - Function | |||||||||
Biological species | Vibrio alginolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Sun, Y.F. / Zhang, W. | |||||||||
Funding support | China, 2items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: The novel amylase function of the carboxyl terminal domain of Amy63. Authors: Sun, Y. / Liu, G. / Liu, G. / Tang, H. / Sun, C. / Zhang, W. / Chen, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jjm.cif.gz | 283.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jjm.ent.gz | 180.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/8jjm ftp://data.pdbj.org/pub/pdb/validation_reports/jj/8jjm | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56005.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2UQL4 #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.48 Å3/Da / Density % sol: 50.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 70% MPD, pH8.0 |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.8→35.79 Å / Num. obs: 101586 / % possible obs: 90.73 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1084 / Net I/σ(I): 12.26 | |||||||||||||||
Reflection shell | Resolution: 1.803→1.868 Å / Num. unique obs: 101586 / CC1/2: 0.994 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.79 Å / SU ML: 0.1505 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8424 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.79 Å
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Refine LS restraints |
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LS refinement shell |
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