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Yorodumi- PDB-5yat: Crystal structure of mitochondrial alcohol dehydrogenase isozyme ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yat | ||||||
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Title | Crystal structure of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115 | ||||||
Components | Mitochondrial alcohol dehydrogenase isozyme III | ||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase / catalytic zinc / yeast / dimer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Komagataella phaffii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.745 Å | ||||||
Authors | Zhang, H.D. / Li, Q. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: Investigation of structure and function of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115. Authors: Zhang, H. / Li, Q. / Wang, L. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yat.cif.gz | 264.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yat.ent.gz | 216.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yat_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 5yat_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 5yat_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 5yat_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/5yat ftp://data.pdbj.org/pub/pdb/validation_reports/ya/5yat | HTTPS FTP |
-Related structure data
Related structure data | 4w6zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37038.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-1_0472 / Production host: Pichia (fungus) / References: UniProt: C4R0S8 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-ZN / #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: 52.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 13% (v/v) 2-propanol, 0.2 M Zinc acetate, 0.1M Sodium cacodylate/Hydrochloric acid, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979158 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979158 Å / Relative weight: 1 |
Reflection | Resolution: 1.745→96.88 Å / Num. obs: 72896 / % possible obs: 99.9 % / Redundancy: 21.9 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 14.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4W6Z Resolution: 1.745→36.613 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.745→36.613 Å
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Refine LS restraints |
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LS refinement shell |
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