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Yorodumi- PDB-3fak: Structural and Functional Analysis of a Hormone-Sensitive Lipase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fak | ||||||
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Title | Structural and Functional Analysis of a Hormone-Sensitive Lipase like EstE5 from a Metagenome Library | ||||||
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: 1.9 Å | ||||||
Authors | Hwang, K.Y. / Nam, K.H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Structural and functional analysis of a novel EstE5 belonging to the subfamily of hormone-sensitive lipase Authors: Nam, K.H. / Kim, M.-Y. / Kim, S.-J. / Priyadarshi, A. / Lee, W.H. / 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 | 3fak.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fak.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fak_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 3fak_full_validation.pdf.gz | 444.7 KB | Display | |
Data in XML | 3fak_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3fak_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/3fak ftp://data.pdbj.org/pub/pdb/validation_reports/fa/3fak | HTTPS FTP |
-Related structure data
Related structure data | 2c7bS S: Starting model for refinement |
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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) Description: soil Metaggenome Library / Plasmid: pET-21a / 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: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: 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 Å3/Da / Density % sol: 38.61 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-HCl pH 7.5, 2.2M ammonium sulfate, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 22282 / Num. obs: 20076 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 2.52 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C7B Resolution: 1.9→19.79 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: the residues 194-197 are with high rmsd, but they were built depending on electron-density map
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Refinement step | Cycle: LAST / Resolution: 1.9→19.79 Å
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Refine LS restraints |
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