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Yorodumi- PDB-6xsv: X-ray structure of a tetragonal crystal form of alpha amylase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xsv | ||||||
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Title | X-ray structure of a tetragonal crystal form of alpha amylase from Aspergillus oryzae (Tala-Amylase) at 1.65 A resolution | ||||||
Components | Alpha-amylase | ||||||
Keywords | SUGAR BINDING PROTEIN / substrate complex / Novo lipase / catalytic site / ligands | ||||||
Function / homology | Function and homology information cell wall-bounded periplasmic space / hyphal septin band / spitzenkorper / fungal-type cell wall / alpha-amylase / cell septum / carbohydrate catabolic process / alpha-amylase activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | McPherson, A. | ||||||
Citation | Journal: J.Biosci.Bioeng. / Year: 2021 Title: Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase). Authors: Gee, C.L. / Holton, J.M. / McPherson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xsv.cif.gz | 202.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xsv.ent.gz | 159 KB | Display | PDB format |
PDBx/mmJSON format | 6xsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xsv ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xsv | HTTPS FTP |
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-Related structure data
Related structure data | 6xsjC 2taaS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54812.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: rhaG, amy3, OAory_01056410 / Production host: Aspergillus oryzae (mold) References: UniProt: B0FZ76, UniProt: P0C1B3*PLUS, alpha-amylase |
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-Sugars , 2 types, 4 molecules
#2: Sugar | #4: Sugar | |
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-Non-polymers , 4 types, 517 molecules
#3: Chemical | #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.47 Å3/Da / Density % sol: 50.1 % / Description: elongated rectangular prisms |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystals grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1 M MES buffer at pH 6.5. Drops composed of equal amounts of the protein at 30 ...Details: Crystals grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1 M MES buffer at pH 6.5. Drops composed of equal amounts of the protein at 30 mg/ml in water with the reservoir solution. Crystals grew after about 0ne to two weeks at 298 K PH range: 6 - 7.247 |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→66.45 Å / Num. obs: 66065 / % possible obs: 99.8 % / Redundancy: 124.3 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.027 / Rrim(I) all: 0.141 / Rsym value: 0.128 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 41 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3098 / CC1/2: 0.19 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2TAA Resolution: 1.65→66.45 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 23.22 / Stereochemistry target values: ML Details: Structure was refined to convergence in REFMAC then passed through ten runs of COOT rebuilding and REFINE from PHENIX.
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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 max: 138.31 Å2 / Biso mean: 43.223 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→66.45 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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