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Yorodumi- PDB-3g9z: Crystal structure of EstE5, was soaked by p-nitrophenyl caprylate -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g9z | ||||||
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Title | Crystal structure of EstE5, was soaked by p-nitrophenyl caprylate | ||||||
Components | Esterase/lipase | ||||||
Keywords | HYDROLASE / HSL / EstE5 / esterase / lipase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Hwang, K.Y. / Nam, K.H. | ||||||
Citation | Journal: To be Published Title: Structural and biological characterization of EstE5 Authors: Hwang, K.Y. / 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 | 3g9z.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g9z.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 3g9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g9z_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 3g9z_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 3g9z_validation.xml.gz | 13 KB | Display | |
Data in CIF | 3g9z_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/3g9z ftp://data.pdbj.org/pub/pdb/validation_reports/g9/3g9z | HTTPS FTP |
-Related structure data
Related structure data | 3g9tC 3g9uC 3fakS 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: 34647.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: estE5 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q0GMU2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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#2: 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: 1.94 Å3/Da / Density % sol: 36.75 % |
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-HCl pH 7.0-7.5, 1.8-2.2M ammonium sulfate, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K PH range: 7.0-7.5 |
-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 315 / Detector: CCD / Date: Dec 18, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 14373 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Num. measured all: 147406 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FAK Resolution: 2.2→37.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.484 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 73.58 Å2 / Biso mean: 41.6 Å2 / Biso min: 24.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→37.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -15.5696 Å / Origin y: -17.8961 Å / Origin z: 36.2852 Å
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