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Yorodumi- PDB-6m4k: X-ray crystal structure of wild type alpha-amylase I from Eisenia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m4k | ||||||
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Title | X-ray crystal structure of wild type alpha-amylase I from Eisenia fetida | ||||||
Components | Alpha-amylase | ||||||
Keywords | HYDROLASE / TIM barrel / GH family 13 / carbohydrase / cold-active | ||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Eisenia fetida (common brandling worm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Hirano, Y. / Tsukamoto, K. / Ariki, S. / Naka, Y. / Ueda, M. / Tamada, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: X-ray crystallographic structural studies of alpha-amylase I from Eisenia fetida. Authors: Hirano, Y. / Tsukamoto, K. / Ariki, S. / Naka, Y. / Ueda, M. / Tamada, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m4k.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m4k.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 6m4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m4k ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m4k | HTTPS FTP |
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-Related structure data
Related structure data | 6m4lC 6m4mC 1kxqS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 58349.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eisenia fetida (common brandling worm) / Gene: alpha-amylase / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A173N065, alpha-amylase |
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-Non-polymers , 7 types, 744 molecules
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | ChemComp-CL / | ||||||
#4: Chemical | ChemComp-ACT / | ||||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-1PE / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.79 Å3/Da / Density % sol: 55.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.3 M lithium sulfate, 3% (v/v) PEG 400, 0.1 M magnesium chloride, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→49.2203 Å / Num. obs: 160191 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 16.5515777525 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.056 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 7805 / CC1/2: 0.847 / Rrim(I) all: 0.965 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KXQ Resolution: 1.3→49.22 Å / SU ML: 0.112884114388 / Cross valid method: FREE R-VALUE / σ(F): 1.33016062502 / Phase error: 18.9317217916 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: 20.1494242133 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→49.22 Å
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Refine LS restraints |
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LS refinement shell |
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