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- PDB-7atd: Structure of inactive EstD11 S144A in complex with methyl-naproxen -
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Open data
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Basic information
Entry | Database: PDB / ID: 7atd | |||||||||
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Title | Structure of inactive EstD11 S144A in complex with methyl-naproxen | |||||||||
![]() | EstD11 S144A | |||||||||
![]() | HYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure | |||||||||
Function / homology | ACETATE ION / FORMIC ACID / Naproxen Methyl Ester![]() | |||||||||
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 | ![]() | 146.6 KB | Display | ![]() |
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PDB format | ![]() | 113.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7at0SC ![]() 7at2C ![]() 7at3C ![]() 7at4C ![]() 7atfC ![]() 7atqC ![]() 7auyC ![]() 7av5C ![]() 7nb5C 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 2 - 296 / Label seq-ID: 2 - 296
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Components
#1: Protein | Mass: 32170.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-FMT / #3: Chemical | #4: Chemical | ChemComp-RXH / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 3.2M Sodium formate + 0.1M citrate pH 5 / PH range: 5 |
-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: Mar 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→48.38 Å / Num. obs: 99895 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.047 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.752 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4827 / CC1/2: 0.53 / Rpim(I) all: 0.57 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7AT0 Resolution: 1.45→45.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.5 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.72 Å2 / Biso mean: 18.971 Å2 / Biso min: 9.02 Å2
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Refinement step | Cycle: final / Resolution: 1.45→45.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9638 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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