+Open data
-Basic information
Entry | Database: PDB / ID: 7at3 | ||||||
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Title | Structure of EstD11 in complex with Naproxen and methanol | ||||||
Components | EstD11 | ||||||
Keywords | HYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure | ||||||
Function / homology | FORMIC ACID / METHANOL / (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: 1.4 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 | 7at3.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7at3.ent.gz | 115.3 KB | Display | PDB format |
PDBx/mmJSON format | 7at3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7at3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7at3_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7at3_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 7at3_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7at3 ftp://data.pdbj.org/pub/pdb/validation_reports/at/7at3 | HTTPS FTP |
-Related structure data
Related structure data | 7at0SC 7at2C 7at4C 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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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) #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: 2.18 Å3/Da / Density % sol: 43.55 % |
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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: Oct 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.35 Å / Num. obs: 111559 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.034 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.155 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5471 / CC1/2: 0.66 / Rpim(I) all: 0.383 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AT0 Resolution: 1.4→45.66 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.112 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / 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: 78.87 Å2 / Biso mean: 18.398 Å2 / Biso min: 9.76 Å2
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Refinement step | Cycle: final / Resolution: 1.4→45.66 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9856 / 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: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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