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Yorodumi- PDB-3k6k: Crystal structure at 2.2 angstrom of HSL-homolog EstE7 from a met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k6k | ||||||
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Title | Crystal structure at 2.2 angstrom of HSL-homolog EstE7 from a metagenome library | ||||||
Components | Esterase/lipase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Hwang, K.Y. / Nam, K.H. | ||||||
Citation | Journal: to be published Title: Biochemical and structural analysis of hormone-sensitive lipase homolog EstE7; Insight into the stabilized dimerization of HSL-homolog proteins Authors: Nam, K.H. / Rhee, K.H. / Lee, W.H. / Jeong, B.-C. / Song, H.K. / Hwang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k6k.cif.gz | 236.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k6k.ent.gz | 191 KB | Display | PDB format |
PDBx/mmJSON format | 3k6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k6k_validation.pdf.gz | 492.9 KB | Display | wwPDB validaton report |
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Full document | 3k6k_full_validation.pdf.gz | 523.6 KB | Display | |
Data in XML | 3k6k_validation.xml.gz | 49.3 KB | Display | |
Data in CIF | 3k6k_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/3k6k ftp://data.pdbj.org/pub/pdb/validation_reports/k6/3k6k | HTTPS FTP |
-Related structure data
Related structure data | 3dnmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | RECENTLY, THE DEPOSITORS HAVE CHARACTERIZED THE OLIGOMERIC STATE OF THIS PROTEIN. THIS PROTEIN REVEALS THE MONOMER AND DIMER FORMATION. BOTH OLIGOMERIC STATE REVEALS THE ENZYME ACTIVITY. BASED ON OUR STUDY, BIOLOGICAL ASSEMBLY OF ESTE7 ARE FORMING THE MONOMER AND DIMER FORMATION. ESPECIALLY, DIMERIC ESTE7 HAVE HIGH ACTIVITY THAN MONOMER ESTE7. |
-Components
#1: Protein | Mass: 34653.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: estE7 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q0GMU1, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-BME / | #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: 3.14 Å3/Da / Density % sol: 60.85 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Bis-Tris propane, pH 7.0, 0.2M ammonium sulfate, 1M lithium 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: 6C1 / Wavelength: 1.23 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 84721 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5 % / Net I/σ(I): 10.09 / Num. measured all: 420468 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.82 / Num. unique all: 7220 / % possible all: 82.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DNM Resolution: 2.2→48.27 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.61 / SU B: 6.723 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES; REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.27 Å2 / Biso mean: 27.307 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.27 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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