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- PDB-7p4w: Crystal structure of alpha-amylase from Aspergillus oryzae in spa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p4w | ||||||
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Title | Crystal structure of alpha-amylase from Aspergillus oryzae in space group I222 | ||||||
![]() | Alpha-amylase | ||||||
![]() | HYDROLASE / amylase / aspergillus / oryzae / alpha-amylase | ||||||
Function / homology | ![]() alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / calcium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bellini, D. / Gorrec, F. | ||||||
![]() | ![]() Title: The FUSION protein crystallization screen. Authors: Gorrec, F. / Bellini, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 80.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 386.4 KB | Display | ![]() |
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Full document | ![]() | 391.2 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p4zC ![]() 6taaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 52351.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-MES / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% PEG 20k, 20% PEG 500mme, 0.1 M MES/Imidazole pH 6.5, 20 mM of each Polyamine (Morpheus Fusion screen, well H11) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→51.92 Å / Num. obs: 32915 / % possible obs: 99.7 % / Redundancy: 9.2 % / Biso Wilson estimate: 36.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 9.9 / Rpim(I) all: 0.17 / Rrim(I) all: 4.9 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.28→2.32 Å / Rmerge(I) obs: 2.27 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1549 / CC1/2: 0.27 / Rpim(I) all: 1.1 / Rrim(I) all: 2.53 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6TAA Resolution: 2.28→51.91 Å / SU ML: 0.4488 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3493 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: 53.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→51.91 Å
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Refine LS restraints |
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LS refinement shell |
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