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- PDB-6sav: Structural and functional characterisation of three novel fungal ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sav | ||||||
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Title | Structural and functional characterisation of three novel fungal amylases with enhanced stability and pH tolerance | ||||||
![]() | (Alpha-amylase) x 2 | ||||||
![]() | HYDROLASE / biotechnology / fungal amylase | ||||||
Function / homology | ![]() alpha-amylase activity => GO:0004556 / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / calcium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roth, C. / Moroz, O.V. / Turkenburg, J.P. / Blagova, E. / Waterman, J. / Ariza, A. / Ming, L. / Tianqi, S. / Andersen, C. / Davies, G.J. / Wilson, K.S. | ||||||
![]() | ![]() Title: Structural and Functional Characterization of Three Novel Fungal Amylases with Enhanced Stability and pH Tolerance. Authors: Roth, C. / Moroz, O.V. / Turkenburg, J.P. / Blagova, E. / Waterman, J. / Ariza, A. / Ming, L. / Tianqi, S. / Andersen, C. / Davies, G.J. / Wilson, K.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217.4 KB | Display | ![]() |
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PDB format | ![]() | 169.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.1 KB | Display | ![]() |
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Full document | ![]() | 500.5 KB | Display | |
Data in XML | ![]() | 43.5 KB | Display | |
Data in CIF | ![]() | 67.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6saoC ![]() 6sauC ![]() 2taaS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 48268.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 48269.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 1 types, 3 molecules ![](data/chem/img/NAG.gif)
#4: Sugar |
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-Non-polymers , 4 types, 955 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.2 M NaCl, 0.1 M Na-acetate pH 4.6, 30 %MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 17, 2007 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.4→43.21 Å / Num. obs: 146177 / % possible obs: 92.9 % / Redundancy: 2.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.03 / Rrim(I) all: 0.044 / Net I/σ(I): 9.6 / Num. measured all: 315876 / Scaling rejects: 5 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.1 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2taa Resolution: 1.4→39.99 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.92 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 74.22 Å2 / Biso mean: 12.475 Å2 / Biso min: 5.91 Å2
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Refinement step | Cycle: final / Resolution: 1.4→39.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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