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- PDB-3qoo: Crystal structure of hot-dog-like Taci_0573 protein from Thermana... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qoo | ||||||
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Title | Crystal structure of hot-dog-like Taci_0573 protein from Thermanaerovibrio acidaminovorans | ||||||
![]() | Uncharacterized protein | ||||||
![]() | Structural genomics / Unknown function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / hot-dog superfamily | ||||||
Function / homology | Fluoroacetyl-CoA thioesterase / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Michalska, K. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal structure of hot-dog-like Taci_0573 protein from Thermanaerovibrio acidaminovorans Authors: Michalska, K. / Li, H. / Clancy, S. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.8 KB | Display | ![]() |
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PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.7 KB | Display | ![]() |
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Full document | ![]() | 420.9 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
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Components
#1: Protein | Mass: 15518.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 6589 / Gene: Taci_0573 / Plasmid: pMCSG7 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M MgCl2, 0.1 M sodium citrate, 40% PEG400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791829 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. all: 34231 / Num. obs: 34179 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. There is a strong positive peak in Fo-Fc electron density map near Lys126 most likely corresponding to a small ligand molecule but we were ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. There is a strong positive peak in Fo-Fc electron density map near Lys126 most likely corresponding to a small ligand molecule but we were unable to unambiguously identify and model it.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.416 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→47.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.251→1.284 Å / Total num. of bins used: 20
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