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- PDB-5a2b: Crystal Structure of Anoxybacillus Alpha-amylase Provides Insight... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a2b | |||||||||
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Title | Crystal Structure of Anoxybacillus Alpha-amylase Provides Insights into a New Glycosyl Hydrolase Subclass | |||||||||
![]() | ANOXYBACILLUS ALPHA-AMYLASE | |||||||||
![]() | HYDROLASE / CALCIUM-BINDING SITE / GEOBACILLUS / GLYCOSYL HYDROLASE | |||||||||
Function / homology | ![]() alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ng, C.L. / Chai, K.P. / Othman, N.F. / Teh, A.H. / Ho, K.L. / Chan, K.G. / Goh, K.M. | |||||||||
![]() | ![]() Title: Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into Maltose Binding of a New Glycosyl Hydrolase Subclass. Authors: Chai, K.P. / Othman, N.F.B. / Teh, A. / Ho, K.L. / Chan, K. / Shamsir, M.S. / Goh, K.M. / Ng, C.L. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.2 KB | Display | ![]() |
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PDB format | ![]() | 175.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 806.5 KB | Display | ![]() |
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Full document | ![]() | 809.6 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a2aC ![]() 5a2cC ![]() 4e2oS C: citing same article ( S: Starting model for refinement |
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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: 58164.398 Da / Num. of mol.: 1 / Fragment: TRUNCATED PROTEIN, RESIDUES 24-478 Source method: isolated from a genetically manipulated source Details: CATALYTIC DOMAIN A WITH TIM BARREL FOLD (RESIDUES 26 TO 139,187 TO 393), DOMAIN B (RESIDUES 140 TO 186), AND DOMAIN C WITH AN ALL-ALPHA-BETA FOLD (RESIDUES 394 TO 475) Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.5 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2 M CALCIUM ACETATE 0.1 M SODIUM CACODYLATE (PH 6.5) 18% (W/V) POLYETHYLENE GLYCOL 8, 000 20 MM MALTOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Jul 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5148 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.6 Å / Num. obs: 43446 / % possible obs: 94.5 % / Observed criterion σ(I): 1.8 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.8 / % possible all: 83.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4E2O Resolution: 1.85→63.35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.101 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
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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: 25.357 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→63.35 Å
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Refine LS restraints |
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