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Yorodumi- PDB-5zwr: Structural Basis for the Enantioselectivity of Est-Y29 toward (S)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zwr | ||||||
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Title | Structural Basis for the Enantioselectivity of Est-Y29 toward (S)-ketoprofen | ||||||
Components | Est-Y29 | ||||||
Keywords | 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 / (2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Ngo, D.T. / Oh, C. / Park, K. / Nguyen, L. / Byun, H.M. / Kim, S. / Yoon, S. / Ryu, Y. / Ryu, B.H. / Kim, T.D. / Kim, K.K. | ||||||
Citation | Journal: Acs Catalysis / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zwr.cif.gz | 190.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zwr.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zwr_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5zwr_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5zwr_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 5zwr_validation.cif.gz | 64 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/5zwr ftp://data.pdbj.org/pub/pdb/validation_reports/zw/5zwr | HTTPS FTP |
-Related structure data
Related structure data | 5zwqC 5zwvC 4p6bS 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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Unit cell |
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-Components
#1: Protein | Mass: 44208.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | #4: 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: 3.29 Å3/Da / Density % sol: 62.58 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.6 Details: containing 1 M sodium citrate and 100 mM sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
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: 1.69→28.94 Å / Num. obs: 127327 / % possible obs: 99.68 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 49.85 |
Reflection shell | Resolution: 1.69→1.75 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P6B Resolution: 1.69→28.94 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 16.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→28.94 Å
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Refine LS restraints |
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LS refinement shell |
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