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Open data
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Basic information
Entry | Database: PDB / ID: 7auy | ||||||
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Title | Structure of EstD11 in complex with Fluorescein | ||||||
![]() | EstD11 | ||||||
![]() | HYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure | ||||||
Function / homology | FLUORESCIN / FORMIC ACID![]() | ||||||
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 | ![]() | 115.5 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7at0SC ![]() 7at2C ![]() 7at3C ![]() 7at4C ![]() 7atdC ![]() 7atfC ![]() 7atqC ![]() 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: SER / Beg label comp-ID: SER / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 3 - 295 / Label seq-ID: 3 - 295
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Components
#1: Protein | Mass: 32186.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET22 / Production host: ![]() ![]() #2: Chemical | ChemComp-FMT / | #3: Chemical | ChemComp-FDS / #4: 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: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3.2M Sodium formate + 0.1M citric acid pH 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: Jul 11, 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: 2.28→48.18 Å / Num. obs: 26303 / % possible obs: 97.6 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.051 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2581 / CC1/2: 0.509 / Rpim(I) all: 0.627 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7AT0 Resolution: 2.28→45.83 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.595 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.228 / 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: 149.37 Å2 / Biso mean: 58.178 Å2 / Biso min: 25.61 Å2
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Refinement step | Cycle: final / Resolution: 2.28→45.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 7248 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.28→2.339 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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