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Yorodumi- PDB-4j7a: Crystal Structure of Est25 - a Bacterial Homolog of Hormone-Sensi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j7a | ||||||
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Title | Crystal Structure of Est25 - a Bacterial Homolog of Hormone-Sensitive Lipase from a Metagenomic Library | ||||||
Components | Esterase | ||||||
Keywords | HYDROLASE / alpha/beta | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.492 Å | ||||||
Authors | Ngo, T.D. / Ryu, B.H. / Ju, H.S. / Jang, E.J. / Park, K.S. / Joo, S.B. / Kim, K.K. / Kim, D.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural and functional analyses of a bacterial homologue of hormone-sensitive lipase from a metagenomic library Authors: Ngo, T.D. / Ryu, B.H. / Ju, H. / Jang, E. / Park, K. / Kim, K.K. / Kim, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j7a.cif.gz | 564.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j7a.ent.gz | 465.4 KB | Display | PDB format |
PDBx/mmJSON format | 4j7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j7a_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 4j7a_full_validation.pdf.gz | 463.6 KB | Display | |
Data in XML | 4j7a_validation.xml.gz | 70.1 KB | Display | |
Data in CIF | 4j7a_validation.cif.gz | 109.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/4j7a ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j7a | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39744.430 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q4TZQ3 #2: 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: 2.92 Å3/Da / Density % sol: 57.9 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7 Details: 2.4M sodium malonate pH 7.0, Microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 203 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97888, 0.97917, 0.96395, 1.00000 | |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD | |||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.49→50 Å / Num. all: 297211 / Num. obs: 285917 / % possible obs: 96.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 | |||||||||||||||
Reflection shell | Resolution: 1.49→50 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.6 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.492→28.555 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 14.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.492→28.555 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: 30
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