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Yorodumi- PDB-5j7i: Crystal structure of a Geobacillus thermoglucosidasius Acetylatin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j7i | ||||||
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Title | Crystal structure of a Geobacillus thermoglucosidasius Acetylating Aldehyde Dehydrogenase in complex with ADP | ||||||
Components | Acetaldehyde dehydrogenase (Acetylating)Acetaldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Acetylating aldehyde dehydrogenase / complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 4 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 | 5j7i.cif.gz | 960.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j7i.ent.gz | 818.3 KB | Display | PDB format |
PDBx/mmJSON format | 5j7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/5j7i ftp://data.pdbj.org/pub/pdb/validation_reports/j7/5j7i | HTTPS FTP |
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-Related structure data
Related structure data | 5j78SC 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: 52280.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermoglucosidasius (strain C56-YS93) (bacteria) Strain: C56-YS93 / Gene: Geoth_3234 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0M1QQ83, acetaldehyde dehydrogenase (acetylating) #2: Chemical | #3: Chemical | ChemComp-APR / | |
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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: 2.67 Å3/Da / Density % sol: 53.94 % / Description: thin and plate-like |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: protein solution containing 10.7mg/ml protein, 0.5mM acetyl-CoA and 5mM NAD+ was mixed 1:1 with 0.1M MMT buffer pH5.0, 21 to 23% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 14328 / % possible obs: 78 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.267 / Net I/σ(I): 3.87 |
Reflection shell | Resolution: 4→4.07 Å / Redundancy: 2.26 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.26 / % possible all: 70.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J78 Resolution: 4→42.668 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.78 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→42.668 Å
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Refine LS restraints |
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LS refinement shell |
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