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Yorodumi- PDB-8x6m: Crystal Structure of Glycerol Dehydrogenase in the Presence of NA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8x6m | ||||||
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Title | Crystal Structure of Glycerol Dehydrogenase in the Presence of NAD+ and Glycerol | ||||||
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 (NAD+) activity / glycerol dehydrogenase / 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 Å | ||||||
Authors | Park, T. / Kang, J.Y. / Jin, M. / Yang, J. / Kim, H. / Noh, C. / Eom, S.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Plos One / Year: 2024 Title: Structural insights into the octamerization of glycerol dehydrogenase. Authors: Park, T. / Kang, J.Y. / Jin, M. / Yang, J. / Kim, H. / Noh, C. / 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 | 8x6m.cif.gz | 158.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x6m.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 8x6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x6m_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8x6m_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8x6m_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 8x6m_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/8x6m ftp://data.pdbj.org/pub/pdb/validation_reports/x6/8x6m | HTTPS FTP |
-Related structure data
Related structure data | 8gobS 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: 39817.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: gldA, b3945, JW5556 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A9S5, glycerol dehydrogenase, (R)-aminopropanol dehydrogenase #2: Chemical | #3: Chemical | #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: 3.62 Å3/Da / Density % sol: 66.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM Na2HPO4-citrate (pH 4.2), 200 mM NaCl, and 10% (w/v) PEG 3000 |
-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: 0.97942 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2→118.1 Å / Num. obs: 78784 / % possible obs: 99.9 % / Redundancy: 26.1 % / CC1/2: 0.999 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2→2 Å / Num. unique obs: 3865 / CC1/2: 0.94 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8GOB Resolution: 2→50.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.869 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 35.575 Å2
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Refinement step | Cycle: 1 / Resolution: 2→50.01 Å
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Refine LS restraints |
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