+Open data
-Basic information
Entry | Database: PDB / ID: 5egn | |||||||||||||||
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Title | Est816 as an N-Acyl homoserine lactone degrading enzyme | |||||||||||||||
Components | Esterase | |||||||||||||||
Keywords | HYDROLASE / N-acyl-homoserine lactone / lactonase / quorum-sensing / thermostability | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | uncultured bacterium (environmental samples) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.636 Å | |||||||||||||||
Authors | Xie, W. / Liu, X. / Cao, L. / Liu, Y. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: To Be Published Title: Est816 as an N-Acyl homoserine lactone degrading enzyme Authors: Xie, W. / Liu, X. / Cao, L. / Liu, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5egn.cif.gz | 393.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5egn.ent.gz | 322.7 KB | Display | PDB format |
PDBx/mmJSON format | 5egn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5egn_validation.pdf.gz | 494.2 KB | Display | wwPDB validaton report |
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Full document | 5egn_full_validation.pdf.gz | 511.9 KB | Display | |
Data in XML | 5egn_validation.xml.gz | 71.7 KB | Display | |
Data in CIF | 5egn_validation.cif.gz | 97.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/5egn ftp://data.pdbj.org/pub/pdb/validation_reports/eg/5egn | HTTPS FTP |
-Related structure data
Related structure data | 2xuaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 29539.189 Da / Num. of mol.: 8 / Fragment: UNP residues 1-261 / Mutation: A216V/K238N Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: est816 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I6YRG4, carboxylesterase #2: 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: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 28% PEG 3350, 0.1M sodium acetate pH 5.6, 0.2M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→50 Å / Num. obs: 57955 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.63→2.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XUA Resolution: 2.636→44.817 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.06 / 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: 2.636→44.817 Å
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Refine LS restraints |
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LS refinement shell |
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