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Yorodumi- PDB-7pzt: Structure of the bacterial toxin, TecA, an asparagine deamidase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pzt | |||||||||
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Title | Structure of the bacterial toxin, TecA, an asparagine deamidase from Alcaligenes faecalis. | |||||||||
Components | Urea amidohydrolaseUrease | |||||||||
Keywords | TOXIN / Asparagine Deamidase / Bacterial Toxin / Effector Protein / Type VI Secretion System / Cys-His Pair / RhoA deamidation | |||||||||
Function / homology | hydrolase activity / Urea amidohydrolase Function and homology information | |||||||||
Biological species | Alcaligenes faecalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å | |||||||||
Authors | 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 | United Kingdom, 2items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pzt.cif.gz | 230.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pzt.ent.gz | 185.7 KB | Display | PDB format |
PDBx/mmJSON format | 7pzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/7pzt ftp://data.pdbj.org/pub/pdb/validation_reports/pz/7pzt | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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.) Alcaligenes faecalis (bacteria) / Gene: D0C27_02010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P8JK46 #2: Chemical | ChemComp-MES / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97106 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.84→57.344 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.185 / SU B: 7.626 / SU ML: 0.114 / Average fsc free: 0.8992 / Average fsc work: 0.9121 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.136 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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