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- PDB-7nb5: Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nb5 | ||||||
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Title | Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester | ||||||
![]() | EstD11 S144A | ||||||
![]() | HYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure | ||||||
Function / homology | Chem-U68![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miguel-Ruano, V. / Rivera, I. / Hermoso, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.4 KB | Display | ![]() |
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PDB format | ![]() | 100.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 687.7 KB | Display | ![]() |
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Full document | ![]() | 690.1 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7at0SC ![]() 7at2C ![]() 7at3C ![]() 7at4C ![]() 7atdC ![]() 7atfC ![]() 7atqC ![]() 7auyC ![]() 7av5C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 32038.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-U68 / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Sodium formate 3.2M and citrate pH 5 0.1M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 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: 2.13→44.84 Å / Num. obs: 15581 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.13→2.19 Å / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 8.2 / Num. unique obs: 1265 / CC1/2: 0.989 / Rpim(I) all: 0.09 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7AT0 Resolution: 2.13→42.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.629 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.253 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→42.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.185 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.576 Å / Origin y: 19.592 Å / Origin z: 16.272 Å
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