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Yorodumi- PDB-3dnm: Crystal Structure Hormone-Sensitive Lipase from a Metagenome Library -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dnm | ||||||
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Title | Crystal Structure Hormone-Sensitive Lipase 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 / Resolution: 2.8 Å | ||||||
Authors | Hwang, K.Y. / Nam, K.H. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Structural and functional analysis of a novel hormone-sensitive lipase from a metagenome library Authors: Nam, K.H. / Kim, M.-Y. / Kim, S.-J. / Priyadarshi, A. / Kwon, S.-T. / Koo, B.-S. / Yoon, S.-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 | 3dnm.cif.gz | 233.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dnm.ent.gz | 188 KB | Display | PDB format |
PDBx/mmJSON format | 3dnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dnm_validation.pdf.gz | 489.4 KB | Display | wwPDB validaton report |
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Full document | 3dnm_full_validation.pdf.gz | 532.8 KB | Display | |
Data in XML | 3dnm_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 3dnm_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/3dnm ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dnm | HTTPS FTP |
-Related structure data
Related structure data | 1lzlS 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 | This protein works in monomer. But crystallographical data shows the dimer protein as reported in some related papers. The depositors consider that the dimer formation is crystallographical data. |
-Components
#1: Protein | Mass: 36006.938 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Description: this protein was purified from Metagenome Library(soil uncultured bacteria) Gene: estE7 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) References: UniProt: Q0GMU1, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Chemical | ChemComp-BME / #3: Chemical | ChemComp-SO4 / #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: 3.01 Å3/Da / Density % sol: 59.19 % |
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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: May 8, 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: 2.8→20 Å / Num. all: 47996 / Num. obs: 42217 / % possible obs: 88 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LZL Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47.8071 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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