+Open data
-Basic information
Entry | Database: PDB / ID: 3v9a | ||||||
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Title | Crystal structure of Esterase/Lipase from uncultured bacterium | ||||||
Components | Esterase/lipase | ||||||
Keywords | HYDROLASE ACTIVATOR / esterase / lipase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å | ||||||
Authors | Kim, I.J. / Nam, K.H. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Esterase/Lipase from uncultured bacterium Authors: Kim, I.J. / Nam, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v9a.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v9a.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 3v9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/3v9a ftp://data.pdbj.org/pub/pdb/validation_reports/v9/3v9a | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 33353.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: estE5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0GMU2 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Tris, pH 7.0, 2.0M ammonium sulfate, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 20, 2009 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 16720 / % possible obs: 92.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.07→2.11 Å / % possible all: 84 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→47.24 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8676 / SU ML: 0.48 / σ(F): 1.5 / Phase error: 20.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.407 Å2 / ksol: 0.366 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.98 Å2 / Biso mean: 37.097 Å2 / Biso min: 17.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→47.24 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: -12.2949 Å / Origin y: 15.2404 Å / Origin z: -0.0296 Å
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Refinement TLS group |
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