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Yorodumi- PDB-8goa: Crystal Structure of Glycerol Dehydrogenase in the absence of NAD+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 8goa | ||||||
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Title | Crystal Structure of Glycerol Dehydrogenase in the absence of NAD+ | ||||||
Components | Glycerol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Glycerol dehydrogenase / complex | ||||||
Function / homology | Function and homology information (R)-aminopropanol dehydrogenase / (R)-aminopropanol dehydrogenase activity / anaerobic glycerol catabolic process / methylglyoxal catabolic process / glycerol dehydrogenase / glycerol dehydrogenase [NAD+] activity / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Park, T. / Hoang, H.N. / Kang, J.Y. / Park, J. / Mun, S.A. / Jin, M. / Yang, J. / Jung, C.-H. / Eom, S.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Febs J. / Year: 2023 Title: Structural and functional insights into the flexible beta-hairpin of glycerol dehydrogenase. Authors: Park, T. / Hoang, H.N. / Kang, J.Y. / Park, J. / Mun, S.A. / Jin, M. / Yang, J. / Jung, C.H. / Eom, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8goa.cif.gz | 286.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8goa.ent.gz | 231 KB | Display | PDB format |
PDBx/mmJSON format | 8goa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/8goa ftp://data.pdbj.org/pub/pdb/validation_reports/go/8goa | HTTPS FTP |
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-Related structure data
Related structure data | 8gobC 5zxlS S: Starting model for refinement C: citing same article (ref.) |
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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: 39817.152 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: gldA, b3945, JW5556 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A9S5, glycerol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-TRS / #4: 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: 5.97 Å3/Da / Density % sol: 79.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium citrate (pH 5.6), 500 mM ammonium sulfate, and 1 M lithium sulfate |
-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 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.24 Å / Num. obs: 86081 / % possible obs: 99.6 % / Redundancy: 8.7 % / CC1/2: 0.99 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.9→2.95 Å / Num. unique obs: 4204 / CC1/2: 0.322 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5zxl Resolution: 2.9→49.24 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.93 Å
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