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- PDB-5zwq: Structural Basis for the Enantioselectivity of Est-Y29 toward (S)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zwq | ||||||
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Title | Structural Basis for the Enantioselectivity of Est-Y29 toward (S)-ketoprofen | ||||||
![]() | Est-Y29 | ||||||
![]() | HYDROLASE / Est-Y29 / esterase / ketoprofen / 2-(3-benzoylphenyl)-propionic acid | ||||||
Function / homology | Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Chem-9KF![]() | ||||||
Biological species | metagenome (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ngo, D.T. / Oh, C. / Park, K. / Nguyen, L. / Byun, H.M. / Kim, S. / Yoon, S. / Ryu, Y. / Ryu, B.H. / Kim, T.D. ...Ngo, D.T. / Oh, C. / Park, K. / Nguyen, L. / Byun, H.M. / Kim, S. / Yoon, S. / Ryu, Y. / Ryu, B.H. / Kim, T.D. / Yang, J.W. / Kim, K.K. | ||||||
![]() | ![]() Title: Structural Basis for the Enantioselectivity of Esterase Est-Y29 toward (S)-Ketoprofen Authors: Ngo, T.D. / Oh, C. / Mizar, P. / Baek, M. / Park, K. / Nguyen, L. / Byeon, H. / Yoon, S. / Ryu, B.H. / Kim, T.D. / Yang, J.W. / Seok, C. / Lee, S.S. / Kim, K.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.2 KB | Display | ![]() |
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PDB format | ![]() | 141.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 57.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44303.516 Da / Num. of mol.: 2 / Mutation: A348V Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Plasmid: pQE30 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | The sequence reference of the protein is not available at UNIPROT at the time of data processing. ...The sequence reference of the protein is not available at UNIPROT at the time of data processing. Residue VAL 348 represented mutation (A348V). | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.63 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.6 / Details: 1 M sodium citrate, 100 mM sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.797→29.13 Å / Num. obs: 105326 / % possible obs: 99.68 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.71 |
Reflection shell | Resolution: 1.797→1.861 Å |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.797→29.13 Å
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Refine LS restraints |
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LS refinement shell |
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