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Yorodumi- PDB-5eht: Indirect contributions of mutations underlie optimization of new ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eht | ||||||
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Title | Indirect contributions of mutations underlie optimization of new enzyme function | ||||||
Components | N-acyl homoserine lactonase | ||||||
Keywords | HYDROLASE / N-Acyl-Homoserine Lactonase / Directed evolution / AiiA / QQL / Lactonase / Phosphatase / Paraoxonase | ||||||
Function / homology | Function and homology information lactone catabolic process / acyl-L-homoserine-lactone lactonohydrolase activity / quorum-quenching N-acyl-homoserine lactonase / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Jackson, C.J. / Hong, N.-S. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects. Authors: Yang, G. / Hong, N. / Baier, F. / Jackson, C.J. / Tokuriki, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eht.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eht.ent.gz | 103.2 KB | Display | PDB format |
PDBx/mmJSON format | 5eht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eht_validation.pdf.gz | 451.6 KB | Display | wwPDB validaton report |
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Full document | 5eht_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 5eht_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5eht_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/5eht ftp://data.pdbj.org/pub/pdb/validation_reports/eh/5eht | HTTPS FTP |
-Related structure data
Related structure data | 5eh9SC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28468.330 Da / Num. of mol.: 1 / Mutation: I9V, S20F, L33V, F64(CSO), V69G, K139T, I230M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: aiiA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A3FJ64, quorum-quenching N-acyl-homoserine lactonase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% (w/v) PEG 4 K, 20% (v/v) glycerol, 80 mM Tris-HCl, pH 8.5, 160 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→32.49 Å / Num. obs: 61760 / % possible obs: 99.47 % / Redundancy: 13.4 % / Net I/σ(I): 20.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EH9 Resolution: 1.29→32.49 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.743 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.115 Å2
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Refinement step | Cycle: 1 / Resolution: 1.29→32.49 Å
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Refine LS restraints |
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