+Open data
-Basic information
Entry | Database: PDB / ID: 3wn6 | ||||||
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Title | Crystal structure of alpha-amylase AmyI-1 from Oryza sativa | ||||||
Components | Alpha-amylase | ||||||
Keywords | HYDROLASE / (alpha/beta)8-barrel / Carbohydrate/Sugar Binding / Glycosylation | ||||||
Function / homology | Function and homology information alpha-amylase activity => GO:0004556 / sucrose catabolic process / starch catabolic process / alpha-amylase / alpha-amylase activity / calcium ion binding Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Ochiai, A. / Sugai, H. / Harada, K. / Tanaka, S. / Ishiyama, Y. / Ito, K. / Tanaka, T. / Uchiumi, T. / Taniguchi, M. / Mitsui, T. | ||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2014 Title: Crystal structure of alpha-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability Authors: Ochiai, A. / Sugai, H. / Harada, K. / Tanaka, S. / Ishiyama, Y. / Ito, K. / Tanaka, T. / Uchiumi, T. / Taniguchi, M. / Mitsui, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wn6.cif.gz | 369.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wn6.ent.gz | 298.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wn6_validation.pdf.gz | 489.3 KB | Display | wwPDB validaton report |
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Full document | 3wn6_full_validation.pdf.gz | 510.7 KB | Display | |
Data in XML | 3wn6_validation.xml.gz | 78.7 KB | Display | |
Data in CIF | 3wn6_validation.cif.gz | 115.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/3wn6 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/3wn6 | HTTPS FTP |
-Related structure data
Related structure data | 1bg9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 25 - 428 / Label seq-ID: 1 - 404
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45342.574 Da / Num. of mol.: 4 / Mutation: G25M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: AMY1.1, AMY1A / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P17654, alpha-amylase |
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-Non-polymers , 5 types, 1664 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-TAR / #5: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG3350, 2% tacsimate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 23, 2013 | |||||||||||||||
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 97842 / % possible obs: 98.4 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 22.6 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.9 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BG9 Resolution: 2.16→48.32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.644 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.099 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→48.32 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.162→2.219 Å / Total num. of bins used: 20
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