+Open data
-Basic information
Entry | Database: PDB / ID: 6keu | ||||||
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Title | Wildtype E53, a microbial HSL esterase | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / esterase / Hormone-sensitive lipase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Erythrobacter longus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Yang, X.C. / Li, Z.Y. / Xu, X.W. / Li, J.X. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Wildtype E53, a microbial HSL esterase Authors: Yang, X.C. / Yingyi, H. / Li, Z.Y. / Shuling, J. / Zhen, R. / Zhao, W. / Henglin, C. / Li, J.X. / 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 | 6keu.cif.gz | 340.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6keu.ent.gz | 219.8 KB | Display | PDB format |
PDBx/mmJSON format | 6keu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6keu_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6keu_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6keu_validation.xml.gz | 61.6 KB | Display | |
Data in CIF | 6keu_validation.cif.gz | 93.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/6keu ftp://data.pdbj.org/pub/pdb/validation_reports/ke/6keu | HTTPS FTP |
-Related structure data
Related structure data | 4ypvS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 32811.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Erythrobacter longus (bacteria) / References: UniProt: A0A074MDU6 |
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-Non-polymers , 6 types, 1564 molecules
#2: Chemical | ChemComp-D8F / ( #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-6NA / | #7: 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: 3.9 Å3/Da / Density % sol: 68.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG MME550, Bis-Tris, Calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 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: 1.99→47.8 Å / Num. obs: 139433 / % possible obs: 99.79 % / Redundancy: 1.92 % / Biso Wilson estimate: 24.82 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 27.42 |
Reflection shell | Resolution: 1.99→2.06 Å / Rmerge(I) obs: 0.322 / Num. unique obs: 13627 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YPV Resolution: 1.99→42.49 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 29.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→42.49 Å
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Refine LS restraints |
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LS refinement shell |
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