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- PDB-7pzt: Structure of the bacterial toxin, TecA, an asparagine deamidase f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pzt | |||||||||
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Title | Structure of the bacterial toxin, TecA, an asparagine deamidase from Alcaligenes faecalis. | |||||||||
![]() | Urea amidohydrolase | |||||||||
![]() | TOXIN / Asparagine Deamidase / Bacterial Toxin / Effector Protein / Type VI Secretion System / Cys-His Pair / RhoA deamidation | |||||||||
Function / homology | hydrolase activity / Urea amidohydrolase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dix, S.R. / Aziz, A.A. / Baker, P.J. / Evans, C.A. / Dickman, M.J. / Farthing, R.J. / King, Z.L.S. / Nathan, S. / Partridge, L.J. / Raih, F.M. ...Dix, S.R. / Aziz, A.A. / Baker, P.J. / Evans, C.A. / Dickman, M.J. / Farthing, R.J. / King, Z.L.S. / Nathan, S. / Partridge, L.J. / Raih, F.M. / Sedelnikova, S.E. / Thomas, M.S. / Rice, D.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of A. faecalis TecA provides insights into its role as an asparagine deamidase toxin which targets RhoA Authors: Dix, S.R. / Aziz, A.A. / Baker, B.J. / Evans, C.A. / Dickman, M.J. / Farthing, R.J. / King, Z.L.S. / Nathan, S. / Partridge, L.J. / Raih, F.M. / Sedelnikova, S.E. / Thomas, M.S. / Rice, D.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.7 KB | Display | ![]() |
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PDB format | ![]() | 185.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.7 KB | Display | ![]() |
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Full document | ![]() | 434.4 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 17682.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MES / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.06 M divalents (0.3 M MgCl2.6H2O + 0.3 M CaCl2.2H2O), 0.1 M buffer system 1 (1.0 M Imidazole, 1.0 M MES monohydrate) pH 6.5, 30 % v/v precipitant mix 1 (40 % v/v PEG 500 MME, 20 % w/v PEG 20000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97106 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→57.31 Å / Num. obs: 28829 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.989 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.84→1.87 Å / Num. unique obs: 1399 / CC1/2: 0.681 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→57.344 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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