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Yorodumi- PDB-5t13: Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t13 | ||||||
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Title | Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel | ||||||
Components | Cyanuric acid amidohydrolase | ||||||
Keywords | HYDROLASE / TrzD - cyanuric acid hydrolase from Acidovorax citrulli / AtzD - cyanuric acid hydrolase from Pseudomonas sp ADP / ACAH - cyanuric acid hydrolase from Azorhizobium calindulans. | ||||||
Function / homology | Function and homology information cyanuric acid amidohydrolase / cyanuric acid amidohydrolase activity / atrazine catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Bera, A.K. / Wackett, L.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel. Authors: Bera, A.K. / Aukema, K.G. / Elias, M. / Wackett, L.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t13.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t13.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 5t13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/5t13 ftp://data.pdbj.org/pub/pdb/validation_reports/t1/5t13 | HTTPS FTP |
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-Related structure data
Related structure data | 4bvqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40292.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: trzD / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3V4, cyanuric acid amidohydrolase | ||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.2, 30% Pentaerythritol ethoxylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03322 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→29.45 Å / Num. obs: 19361 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.19→2.26 Å / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.76 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BVQ Resolution: 2.19→29.45 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→29.45 Å
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Refine LS restraints |
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LS refinement shell |
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