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Yorodumi- PDB-4ftw: Crystal structure of a carboxyl esterase N110C/L145H at 2.3 angst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ftw | ||||||
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Title | Crystal structure of a carboxyl esterase N110C/L145H at 2.3 angstrom resolution | ||||||
Components | Phospholipase/Carboxylesterase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase superfamily / esterase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wu, L. / Ma, J. / Zhou, J. / Yu, H. | ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2013 Title: Enhanced enantioselectivity of a carboxyl esterase from Rhodobacter sphaeroides by directed evolution. Authors: Ma, J. / Wu, L. / Guo, F. / Gu, J. / Tang, X. / Jiang, L. / Liu, J. / Zhou, J. / Yu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ftw.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ftw.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ftw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/4ftw ftp://data.pdbj.org/pub/pdb/validation_reports/ft/4ftw | HTTPS FTP |
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-Related structure data
Related structure data | 4fhzSC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 29919.902 Da / Num. of mol.: 1 / Mutation: N110C/L145H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: CGMCC1.1737, RHOS4_13150, RSP_2728 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3J2V1, carboxylesterase |
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#3: Sugar | ChemComp-3CM / |
-Non-polymers , 4 types, 25 molecules
#2: Chemical | ChemComp-PIN / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-CL / |
#6: 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: 3.49 Å3/Da / Density % sol: 64.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.3M Na-tartrate, 34.5mM CYMAL-3, 0.1M pipes , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: 2012 | ||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 15208 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 20.538 | ||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FHZ Resolution: 2.3→48.663 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 26.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.139 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→48.663 Å
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Refine LS restraints |
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LS refinement shell |
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