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Yorodumi- PDB-8h2b: Crystal structure of alcohol dehydrogenase from Zobellia galactan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h2b | ||||||
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Title | Crystal structure of alcohol dehydrogenase from Zobellia galactanivorans | ||||||
Components | Alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding Similarity search - Function | ||||||
Biological species | Zobellia galactanivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Brott, S. / Bornscheuer, U.T. / Nam, K.H. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of alcohol dehydrogenase from Zobellia galactanivorans Authors: Brott, S. / Bornscheuer, U.T. / Nam, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h2b.cif.gz | 297.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h2b.ent.gz | 240.6 KB | Display | PDB format |
PDBx/mmJSON format | 8h2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/8h2b ftp://data.pdbj.org/pub/pdb/validation_reports/h2/8h2b | HTTPS FTP |
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-Related structure data
Related structure data | 6ljhS 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
#1: Protein | Mass: 39666.227 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0L712 #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.04 Å3/Da / Density % sol: 39.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, pH 7.5, KCl and PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 76289 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.989 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 3735 / CC1/2: 0.734 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LJH Resolution: 2.1→49.58 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.83 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.45 Å2 / Biso mean: 33.5468 Å2 / Biso min: 7.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→49.58 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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