+Open data
-Basic information
Entry | Database: PDB / ID: 6y9k | ||||||
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Title | Esterase EST8 with transacylase activity | ||||||
Components | Esterase Est8 | ||||||
Keywords | HYDROLASE / AB Hydrolase / Transacetylase / Transacylase | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å | ||||||
Authors | Palm, G.J. / Lammers, M. / Berndt, L. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Sequence-Based Prediction of Promiscuous Acyltransferase Activity in Hydrolases. Authors: Muller, H. / Becker, A.K. / Palm, G.J. / Berndt, L. / Badenhorst, C.P.S. / Godehard, S.P. / Reisky, L. / Lammers, M. / Bornscheuer, U.T. #1: Journal: Tetrahedron: Asymmetry / Year: 2008 Title: Asymmetric synthesis of cis-3,5-diacetoxycyclopent-1-ene using metagenome-derived hydrolases Authors: Bruesehaber, E. / Boettcher, D. / Liebeton, K. / Eck, J. / Naumer, C. / Bornscheuer, U. #2: Journal: Molecular Microbiology / Year: 2010 Title: Enantioselective kinetic resolution of phenylalkyl carboxylic acids using metagenome-derived esterases. Authors: Fernandez-Alvaro, E. / Kourist, R. / Winter, J. / Boettcher, D. / Liebeton, K. / Naumer, C. / Eck, J. / Leggewie, C. / Jaeger, K.-E. / Streit, W. / Bornscheuer, U.T. #3: Journal: Tetrahedron: Asymmetry / Year: 2008 Title: Hydrolase-catalyzed stereoselective preparation of protected a,a-dialkyl-a-hydroxycarboxylic acids Authors: Kourist, R. / Nguyen, G.-S. / Struebing, D. / Boettcher, D. / Liebeton, K. / Naumer, C. / Eck, J. / Bornscheuer, U.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y9k.cif.gz | 235.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y9k.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6y9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y9k_validation.pdf.gz | 448.5 KB | Display | wwPDB validaton report |
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Full document | 6y9k_full_validation.pdf.gz | 460.7 KB | Display | |
Data in XML | 6y9k_validation.xml.gz | 42.1 KB | Display | |
Data in CIF | 6y9k_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/6y9k ftp://data.pdbj.org/pub/pdb/validation_reports/y9/6y9k | HTTPS FTP |
-Related structure data
Related structure data | 4xvcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32465.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: EC: 3.1.1.79 #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: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 29% PEG 4000, 0.1 M ammonium sulphate, 0.1 M sodium citrate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 15, 2019 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.298→49.5 Å / Num. obs: 59126 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.19 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.298→2.43 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 9359 / Rsym value: 1.29 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4xvc Resolution: 2.298→49.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.485 / SU ML: 0.221 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.22 Details: Hydrogens have been added in their 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.923 Å2
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Refinement step | Cycle: LAST / Resolution: 2.298→49.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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