+Open data
-Basic information
Entry | Database: PDB / ID: 7at4 | ||||||
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Title | Structure of EstD11 in complex with Naproxen | ||||||
Components | EstD11 | ||||||
Keywords | HYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure | ||||||
Function / homology | FORMIC ACID / (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Miguel-Ruano, V. / Rivera, I. / Hermoso, J.A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2021 Title: Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. Authors: Miguel-Ruano, V. / Rivera, I. / Rajkovic, J. / Knapik, K. / Torrado, A. / Otero, J.M. / Beneventi, E. / Becerra, M. / Sanchez-Costa, M. / Hidalgo, A. / Berenguer, J. / Gonzalez-Siso, M.I. / ...Authors: Miguel-Ruano, V. / Rivera, I. / Rajkovic, J. / Knapik, K. / Torrado, A. / Otero, J.M. / Beneventi, E. / Becerra, M. / Sanchez-Costa, M. / Hidalgo, A. / Berenguer, J. / Gonzalez-Siso, M.I. / Cruces, J. / Rua, M.L. / Hermoso, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7at4.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7at4.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 7at4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7at4 ftp://data.pdbj.org/pub/pdb/validation_reports/at/7at4 | HTTPS FTP |
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-Related structure data
Related structure data | 7at0SC 7at2C 7at3C 7atdC 7atfC 7atqC 7auyC 7av5C 7nb5C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32186.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Metagenomic library Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: pET22 / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||||
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#2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-NPX / ( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3.2M Sodium formate + 0.1M citrate pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.3 Å / Num. obs: 30890 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1652 / CC1/2: 0.91 / Rpim(I) all: 0.277 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AT0 Resolution: 1.7→45.048 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.105 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.1 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.281 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→45.048 Å
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Refine LS restraints |
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LS refinement shell |
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