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- PDB-6taa: STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6taa | ||||||
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Title | STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD | ||||||
![]() | ALPHA-AMYLASE | ||||||
![]() | HYDROLASE(O-GLYCOSYL) | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Swift, H.J. / Brady, L. / Derewenda, Z.S. / Dodson, E.J. / Turkenburg, J.P. / Wilkinson, A.J. | ||||||
![]() | ![]() Title: Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method. Authors: Swift, H.J. / Brady, L. / Derewenda, Z.S. / Dodson, E.J. / Dodson, G.G. / Turkenburg, J.P. / Wilkinson, A.J. #1: ![]() Title: Calcium Binding in Alpha-Amylases: An X-Ray Diffraction Study at 2.1 Angstroms Resolution of Two Enzymes from Aspergillus Authors: Boel, E. / Brady, L. / Brzozowski, A.M. / Derewenda, Z. / Dodson, G.G. / Jensen, V.J. / Petersen, S.B. / Swift, H. / Thim, L. / Woldike, H.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 83.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.3 KB | Display | ![]() |
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Full document | ![]() | 466.8 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Atom site foot note | 1: RESIDUES 139 AND 341 ARE CIS PROLINES. |
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Components
#1: Protein | Mass: 52525.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P10529, UniProt: P0C1B3*PLUS, alpha-amylase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 23794 / Rmerge(I) obs: 0.048 / Num. measured all: 66210 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→7.7 Å / σ(F): 0 Details: SIDE CHAINS OF RESIDUES ALA 1, ASP 5, AND LYS 36 ARE NOT CLEARLY VISIBLE IN ELECTRON DENSITY MAPS, AND ATOMS HAVE BEEN INCLUDED WITH OCCUPANCY ZERO, GIVING RISE TO NON-IDEAL INTERMOLECULAR ...Details: SIDE CHAINS OF RESIDUES ALA 1, ASP 5, AND LYS 36 ARE NOT CLEARLY VISIBLE IN ELECTRON DENSITY MAPS, AND ATOMS HAVE BEEN INCLUDED WITH OCCUPANCY ZERO, GIVING RISE TO NON-IDEAL INTERMOLECULAR DISTANCES AFTER REFINEMENT.
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Refinement step | Cycle: LAST / Resolution: 2.1→7.7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 7.7 Å / Num. reflection all: 23482 / σ(F): 0 / Rfactor all: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |