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Yorodumi- PDB-5j78: Crystal structure of an Acetylating Aldehyde Dehydrogenase from G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j78 | ||||||
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Title | Crystal structure of an Acetylating Aldehyde Dehydrogenase from Geobacillus thermoglucosidasius | ||||||
Components | Acetaldehyde dehydrogenase (Acetylating)Acetaldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Acetylating aldehyde dehydrogenase | ||||||
Function / homology | Function and homology information acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Geobacillus thermoglucosidasius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Crennell, S.J. / Extance, J.P. / Danson, M.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2016 Title: Structure of an acetylating aldehyde dehydrogenase from the thermophilic ethanologen Geobacillus thermoglucosidasius. Authors: Extance, J. / Danson, M.J. / Crennell, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j78.cif.gz | 699 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j78.ent.gz | 584.8 KB | Display | PDB format |
PDBx/mmJSON format | 5j78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/5j78 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/5j78 | HTTPS FTP |
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-Related structure data
Related structure data | 5j7iC 3k9dS 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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Unit cell |
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-Components
#1: Protein | Mass: 52270.883 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The strain used is from Geobacillus thermoglucosidasius NCIMB 11955 Source: (gene. exp.) Geobacillus thermoglucosidasius (bacteria) Strain: NCIMB 11955 / Gene: AcAldDH / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0M1QQ83, acetaldehyde dehydrogenase (acetylating) #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MG / #5: 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: 52.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1M sodium acetate pH 4.8, 0.2M MgCl2, 15% (v/v) PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 123787 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.23 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K9D Resolution: 2.1→49.289 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.289 Å
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Refine LS restraints |
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LS refinement shell |
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