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Yorodumi- PDB-6gmu: Serum paraoxonase-1 by directed evolution with the L69G/H134R/F22... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gmu | ||||||
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Title | Serum paraoxonase-1 by directed evolution with the L69G/H134R/F222S/T332S mutations | ||||||
Components | Serum Paraoxonase-1 by directed evolution with the L69G/H134R/F222S/T332S mutations | ||||||
Keywords | HYDROLASE / beta-propeller / Lactonase / HDL / Organophosphate-hydrolase | ||||||
Function / homology | TolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ben-David, M. / Sussman, J.L. / Tawfik, D.S. | ||||||
Citation | Journal: Mol.Biol.Evol. / Year: 2020 Title: Enzyme Evolution: An Epistatic Ratchet versus a Smooth Reversible Transition. Authors: Ben-David, M. / Soskine, M. / Dubovetskyi, A. / Cherukuri, K.P. / Dym, O. / Sussman, J.L. / Liao, Q. / Szeler, K. / Kamerlin, S.C.L. / Tawfik, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gmu.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gmu.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/6gmu ftp://data.pdbj.org/pub/pdb/validation_reports/gm/6gmu | HTTPS FTP |
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-Related structure data
Related structure data | 6g82C 6h0aC 3srgS 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
#1: Protein | Mass: 39492.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 1. There is no entry for this protein in the Uniprot, since the protein is a chimera (recombinant protein) of four genes (human, rabbit, mouse and rat). 2. The first 17 aa at the N-term is ...Details: 1. There is no entry for this protein in the Uniprot, since the protein is a chimera (recombinant protein) of four genes (human, rabbit, mouse and rat). 2. The first 17 aa at the N-term is missing due to lack of electron density. Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-B3P / | #5: 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: 3.99 Å3/Da / Density % sol: 69.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis-Tris Propane pH 6.5, 0.2M Sodium Bromide and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 18335 / % possible obs: 99.9 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.045 / Rrim(I) all: 0.163 / Net I/σ(I): 16.53 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 881 / CC1/2: 0.927 / Rpim(I) all: 0.238 / Rrim(I) all: 0.886 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SRG Resolution: 2.7→33.308 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→33.308 Å
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Refine LS restraints |
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LS refinement shell |
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