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Yorodumi- PDB-6aae: Crystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aae | ||||||||||||
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Title | Crystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136 | ||||||||||||
Components | Esterase | ||||||||||||
Keywords | HYDROLASE / Chloramphenicol / metagenome / hornome sensitive lipase / HSL / EstDL136 / esterase | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | uncultured bacterium (environmental samples) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.641 Å | ||||||||||||
Authors | Kim, S.H. / Kang, P.A. / Han, K.T. / Lee, S.W. / Rhee, S.K. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: PLoS ONE / Year: 2019 Title: Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome. Authors: Kim, S.H. / Kang, P.A. / Han, K.T. / Lee, S.W. / Rhee, S.K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aae.cif.gz | 145.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aae.ent.gz | 112.8 KB | Display | PDB format |
PDBx/mmJSON format | 6aae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/6aae ftp://data.pdbj.org/pub/pdb/validation_reports/aa/6aae | HTTPS FTP |
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-Related structure data
Related structure data | 6ieyC 1u4nS 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: 34229.297 Da / Num. of mol.: 2 / Mutation: 37-39 deletion Source method: isolated from a genetically manipulated source Details: To make EstDL136 crystal, internal residues from P37 to P39 were deleted Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: estDL136 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G3CR02, carboxylesterase #2: Chemical | ChemComp-1PE / #3: Chemical | ChemComp-PEG / #4: 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: 2.95 Å3/Da / Density % sol: 58.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 500mM Ammonium fluoride (pH6.5), 30% PEG3350, 5% glycerol and 120mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. obs: 100067 / % possible obs: 100 % / Redundancy: 14.3 % / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.64→1.7 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U4N Resolution: 1.641→32.258 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.641→32.258 Å
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Refine LS restraints |
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LS refinement shell |
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