+Open data
-Basic information
Entry | Database: PDB / ID: 5gmx | ||||||
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Title | Crystal structure of a family VIII carboxylesterase | ||||||
Components | Carboxylesterase | ||||||
Keywords | HYDROLASE / EstSRT1 / extended spectrum beta-lactamase activity / flexibility | ||||||
Function / homology | methyl indole-3-acetate esterase activity / carboxylesterase / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / phenylmethanesulfonic acid / Carboxylesterase Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | An, Y.J. / Cha, S.S. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2016 Title: Crystal structure of EstSRT1, a family VIII carboxylesterase displaying hydrolytic activity toward oxyimino cephalosporins Authors: Cha, S.S. / An, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gmx.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gmx.ent.gz | 125.4 KB | Display | PDB format |
PDBx/mmJSON format | 5gmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/5gmx ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gmx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43406.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2RKR9, carboxylesterase #2: Chemical | #3: 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: 2.28 Å3/Da / Density % sol: 46.06 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.5 Details: 25% w/v polyethylene glycol 3350, 100 mM HEPES, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97903 Å |
Detector | Type: RAYONIX MX / Detector: CCD / Date: Jun 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 52188 / % possible obs: 99.3 % / Redundancy: 4.5 % / Rsym value: 0.106 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2→2.03 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→44.241 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 20.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→44.241 Å
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Refine LS restraints |
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LS refinement shell |
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