+Open data
-Basic information
Entry | Database: PDB / ID: 7atf | ||||||
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Title | Structure of EstD11 in complex with p-Nitrophenol | ||||||
Components | EstD11 | ||||||
Keywords | HYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure | ||||||
Function / homology | ACETATE ION / FORMIC ACID / P-NITROPHENOL Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 | 7atf.cif.gz | 153.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7atf.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 7atf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7atf_validation.pdf.gz | 980.2 KB | Display | wwPDB validaton report |
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Full document | 7atf_full_validation.pdf.gz | 986.3 KB | Display | |
Data in XML | 7atf_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 7atf_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7atf ftp://data.pdbj.org/pub/pdb/validation_reports/at/7atf | HTTPS FTP |
-Related structure data
Related structure data | 7at0SC 7at2C 7at3C 7at4C 7atdC 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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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: 32186.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | ChemComp-FMT / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.17 Å3/Da / Density % sol: 43.35 % |
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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: Nov 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→48.26 Å / Num. obs: 175504 / % possible obs: 100 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.024 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.357 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8574 / CC1/2: 0.646 / Rpim(I) all: 0.49 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AT0 Resolution: 1.2→45.62 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.709 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.041 / 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: 67.54 Å2 / Biso mean: 16.824 Å2 / Biso min: 8.55 Å2
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Refinement step | Cycle: final / Resolution: 1.2→45.62 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 10302 / 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: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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