+Open data
-Basic information
Entry | Database: PDB / ID: 7w8n | ||||||
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Title | Microbial Hormone-sensitive lipase E53 wild type | ||||||
Components | (Lipase) x 2 | ||||||
Keywords | HYDROLASE / Esterase / Microbial Hormone-sensitive lipase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Erythrobacter longus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Yang, X. / Li, Z. / Xu, X. / Li, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Front Microbiol / Year: 2021 Title: Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus . Authors: Ding, Y. / Nie, L. / Yang, X.C. / Li, Y. / Huo, Y.Y. / Li, Z. / Gao, Y. / Cui, H.L. / Li, J. / Xu, X.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w8n.cif.gz | 496.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w8n.ent.gz | 399.5 KB | Display | PDB format |
PDBx/mmJSON format | 7w8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/7w8n ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w8n | HTTPS FTP |
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-Related structure data
Related structure data | 7ci0C 7cihC 4ypvS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 4 molecules ABDC
#1: Protein | Mass: 33158.730 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erythrobacter longus (bacteria) / Gene: EH31_02760 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A074MDU6 #2: Protein | | Mass: 33100.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erythrobacter longus (bacteria) / Gene: EH31_02760 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A074MDU6 |
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-Non-polymers , 12 types, 1519 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-6NA / #6: Chemical | ChemComp-DMS / #7: Chemical | ChemComp-CCN / #8: Chemical | ChemComp-D8F / ( #9: Chemical | #10: Chemical | ChemComp-DIO / | #11: Chemical | ChemComp-BUA / | #12: Chemical | #13: Chemical | ChemComp-NA / | #14: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.82 Å3/Da / Density % sol: 67.8 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: MES pH 6.5, PEG, ammonium sulfate, dioxane, PEG 1000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.71 Å / Num. obs: 203632 / % possible obs: 99.85 % / Redundancy: 2 % / Biso Wilson estimate: 26.03 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 14.19 |
Reflection shell | Resolution: 1.75→1.815 Å / Num. unique obs: 20063 / CC1/2: 0.849 / CC star: 0.958 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YPV Resolution: 1.75→48.71 Å / SU ML: 0.186 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4426 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→48.71 Å
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Refine LS restraints |
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LS refinement shell |
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