+Open data
-Basic information
Entry | Database: PDB / ID: 7at2 | ||||||
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Title | Crystal structure of inactive EstD11 S144A | ||||||
Components | EstD11 S144A | ||||||
Keywords | HYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 | 7at2.cif.gz | 145.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7at2.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 7at2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7at2_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 7at2_full_validation.pdf.gz | 431.6 KB | Display | |
Data in XML | 7at2_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 7at2_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7at2 ftp://data.pdbj.org/pub/pdb/validation_reports/at/7at2 | HTTPS FTP |
-Related structure data
Related structure data | 7at0C 7at3C 7at4C 7atdC 7atfC 7atqC 7auyC 7av5C 7nb5C 4xvcS C: citing same article (ref.) S: Starting model for refinement |
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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: 32170.012 Da / Num. of mol.: 2 / Mutation: S144A Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli BL21(DE3) (bacteria) #2: Water | ChemComp-HOH / | |
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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: 43.45 % |
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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: 1.072 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 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: 1.44→48.31 Å / Num. obs: 101766 / % possible obs: 99.4 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.037 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.44→1.46 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5003 / CC1/2: 0.713 / Rpim(I) all: 0.325 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XVC Resolution: 1.44→45.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.161 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.066 / 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: 70.21 Å2 / Biso mean: 13.882 Å2 / Biso min: 6.09 Å2
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Refinement step | Cycle: final / Resolution: 1.44→45.77 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9913 / 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: 1.44→1.477 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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