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Yorodumi- PDB-8hap: Crystal structure of thermostable acetaldehyde dehydrogenase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hap | ||||||
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Title | Crystal structure of thermostable acetaldehyde dehydrogenase from hyperthermophilic archaeon Sulfolobus tokodaii | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / thermostability / acetaldehyde / aldehyde / dehydrogenase / archaea | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Similarity search - Function | ||||||
Biological species | Sulfurisphaera tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Mine, S. / Nakabayashi, M. / Ishikawa, K. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: Crystal structure of thermostable acetaldehyde dehydrogenase from the hyperthermophilic archaeon Sulfolobus tokodaii. Authors: Mine, S. / Nakabayashi, M. / Ishikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hap.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hap.ent.gz | 154.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/8hap ftp://data.pdbj.org/pub/pdb/validation_reports/ha/8hap | HTTPS FTP |
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-Related structure data
Related structure data | 3pqaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 52509.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfurisphaera tokodaii (archaea) / Gene: HA332_07780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832TGS5 #2: Chemical | ChemComp-NA7 / [( | #3: Chemical | #4: Chemical | ChemComp-ATR / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.55 Å3/Da / Density % sol: 51.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 100 mM sodium phosphate dibasic/citric acid (pH 4.2), 200 mM sodium chloride, 10% (v/v) polyethylene glycol (PEG) 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.197→86.635 Å / Num. all: 53563 / Num. obs: 53563 / % possible obs: 99 % / Redundancy: 3.4 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.104 / Rsym value: 0.087 / Net I/av σ(I): 7 / Net I/σ(I): 9.9 / Num. measured all: 182293 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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 Starting model: 3PQA Resolution: 2.2→46.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.285 / SU ML: 0.112 / SU R Cruickshank DPI: 0.2264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.2 Å2 / Biso mean: 36.577 Å2 / Biso min: 18.5 Å2
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Refinement step | Cycle: final / Resolution: 2.2→46.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.254 Å / Rfactor Rfree error: 0
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