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Yorodumi- PDB-6m4m: X-ray crystal structure of the E249Q mutan of alpha-amylase I and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m4m | ||||||
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Title | X-ray crystal structure of the E249Q mutan of alpha-amylase I and maltohexaose complex 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: 1.7 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 | 6m4m.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m4m.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 6m4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m4m ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m4m | HTTPS FTP |
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-Related structure data
Related structure data | 6m4kSC 6m4lC 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: 58348.934 Da / Num. of mol.: 1 / Mutation: E249Q 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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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltohexaose |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose |
-Non-polymers , 6 types, 521 molecules
#4: Chemical | ChemComp-CA / | ||||||
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#5: Chemical | ChemComp-CL / | ||||||
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-PG4 / | #8: Chemical | ChemComp-PGE / | #9: 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: 2.8 Å3/Da / Density % sol: 56.13 % |
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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 sulfate, 0.1 M sodium acetat, 10 mM maltohexaose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.4 Å / Num. obs: 72722 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 18.9779772494 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.09 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3840 / CC1/2: 0.822 / Rrim(I) all: 1.064 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M4K Resolution: 1.7→41.92 Å / SU ML: 0.183574193813 / Cross valid method: FREE R-VALUE / σ(F): 1.33660349133 / Phase error: 17.4980157405 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: 20.7025488004 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→41.92 Å
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Refine LS restraints |
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LS refinement shell |
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