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Yorodumi- PDB-6h0a: Serum paraoxonase-1 by directed evolution with the L69G/H115W/H13... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h0a | ||||||
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Title | Serum paraoxonase-1 by directed evolution with the L69G/H115W/H134R/F222S/T332S mutations | ||||||
Components | Serum Paraoxonase-1 by directed evolution with the L69G/H115W/H134R/F222S/T332S mutations | ||||||
Keywords | HYDROLASE / beta-propeller / Lactonase / HDL / Organophosphate-hydrolase | ||||||
Function / homology | TolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / BROMIDE ION / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 6h0a.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h0a.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 6h0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/6h0a ftp://data.pdbj.org/pub/pdb/validation_reports/h0/6h0a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 39540.836 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 16 aa at the N-term are ...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 16 aa at the N-term are missing due to lack of electron density. Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#4: Sugar | ChemComp-LMT / |
-Non-polymers , 5 types, 211 molecules
#2: Chemical | #3: Chemical | ChemComp-B3P / | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-BR / | #7: 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: 4 Å3/Da / Density meas: 69.23 Mg/m3 / 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: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 38094 / % possible obs: 99.95 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.031 / Rrim(I) all: 0.118 / Net I/σ(I): 28.467 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 3 / Num. unique obs: 1853 / CC1/2: 0.867 / Rpim(I) all: 0.238 / Rrim(I) all: 0.92 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.228 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→47.228 Å
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Refine LS restraints |
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LS refinement shell |
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