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Yorodumi- PDB-3ftn: Q165E/S254K Double Mutant Chimera of alcohol dehydrogenase by exc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ftn | ||||||
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Title | Q165E/S254K Double Mutant Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH | ||||||
Components | NADP-dependent alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / oxydoreductase / bacterial alcohol dehydrogenase / domain exchange / chimera / Metal-binding / NADP / Zinc | ||||||
Function / homology | Function and homology information isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Thermoanaerobacter brockii (bacteria) Clostridium beijerinckii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.192 Å | ||||||
Authors | Frolow, F. / Goihberg, E. / Shimon, L. / Burstein, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Biochemical and structural properties of chimeras constructed by exchange of cofactor-binding domains in alcohol dehydrogenases from thermophilic and mesophilic microorganisms. Authors: Goihberg, E. / Peretz, M. / Tel-Or, S. / Dym, O. / Shimon, L. / Frolow, F. / Burstein, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ftn.cif.gz | 569.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ftn.ent.gz | 470.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ftn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/3ftn ftp://data.pdbj.org/pub/pdb/validation_reports/ft/3ftn | 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 , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37854.195 Da / Num. of mol.: 4 / Mutation: Q165E, S254K Source method: isolated from a genetically manipulated source Details: Residues 153-295 inserted from alcohol dehydrogenase of Clostridium beijerinckii Source: (gene. exp.) Thermoanaerobacter brockii (bacteria), (gene. exp.) Clostridium beijerinckii (bacteria) Gene: adh, ADH1 / Plasmid: BS-P58 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-I References: UniProt: P14941, UniProt: P25984, alcohol dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 930 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #6: 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: 2.57 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8 mg/mL protein, 25 mM Tris-HCl, 50 mM NaCl, 0.1 mM DTT, 50 mM ZnCl2 (pH=7.5)] was mixed with 1 microliter of reservoir solution [16% (w/v) PEG8K, 200 mM magnesium acetate tetrahydrate, 100 ...Details: 8 mg/mL protein, 25 mM Tris-HCl, 50 mM NaCl, 0.1 mM DTT, 50 mM ZnCl2 (pH=7.5)] was mixed with 1 microliter of reservoir solution [16% (w/v) PEG8K, 200 mM magnesium acetate tetrahydrate, 100 mM Cacodylate buffer (pH 6.5), vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2003 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 76750 / % possible obs: 97.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.597 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.192→39.18 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 1.37 / σ(F): 0.02 / Phase error: 22.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.419 Å2 / ksol: 0.359 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.563 Å2
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Refinement step | Cycle: LAST / Resolution: 2.192→39.18 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.4141 Å / Origin y: 22.0063 Å / Origin z: 27.8713 Å
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Refinement TLS group | Selection details: all |