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- PDB-2b5d: Crystal structure of the novel alpha-amylase AmyC from Thermotoga... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2b5d | ||||||
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Title | Crystal structure of the novel alpha-amylase AmyC from Thermotoga maritima | ||||||
![]() | alpha-Amylase | ||||||
![]() | HYDROLASE / (beta/alpha)7 barrel | ||||||
Function / homology | immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dickmanns, A. / Ballschmiter, M. / Liebl, W. / Ficner, R. | ||||||
![]() | ![]() Title: Structure of the novel alpha-amylase AmyC from Thermotoga maritima. Authors: Dickmanns, A. / Ballschmiter, M. / Liebl, W. / Ficner, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.5 KB | Display | ![]() |
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PDB format | ![]() | 99.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.3 KB | Display | ![]() |
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Full document | ![]() | 445.9 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 62942.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 4M Na-formiate, 5% isopropanol, 2mM DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 4, 2003 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→30 Å / Num. all: 54781 / Num. obs: 50618 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.4 / Biso Wilson estimate: 49.1 Å2 / Net I/σ(I): 19.1 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 60.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 60.748 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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