+Open data
-Basic information
Entry | Database: PDB / ID: 5hme | ||||||
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Title | Crystal structure of Triazine Hydrolase variant (P214T/Y215H) | ||||||
Components | Triazine hydrolase | ||||||
Keywords | HYDROLASE / amidohydrolase | ||||||
Function / homology | Function and homology information amidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Arthrobacter aurescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å | ||||||
Authors | Sugrue, E. / Carr, P.D. / Jackson, C.J. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases. Authors: Sugrue, E. / Carr, P.D. / Scott, C. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hme.cif.gz | 339.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hme.ent.gz | 278.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/5hme ftp://data.pdbj.org/pub/pdb/validation_reports/hm/5hme | HTTPS FTP |
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-Related structure data
Related structure data | 5hmdC 5hmfC 4lh8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 50097.906 Da / Num. of mol.: 2 / Mutation: P216T, Y217H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: TrzN / Plasmid: petMCSIII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q6SJY7, UniProt: A1RCJ9*PLUS, atrazine chlorohydrolase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.16 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis Tris, 0.1M Ammonium Acetate, 16% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2015 |
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→35.98 Å / Num. obs: 46881 / % possible obs: 99.7 % / Redundancy: 6.4 % / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LH8 Resolution: 2.151→35.979 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.78 / 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: 2.151→35.979 Å
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Refine LS restraints |
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LS refinement shell |
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