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- PDB-8jus: Crystal structure of aspartate semialdehyde dehydrogenase from Po... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jus | ||||||
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Title | Crystal structure of aspartate semialdehyde dehydrogenase from Porphyromonas gingivalis complexed with 2',5'adenosine diphosphate | ||||||
![]() | Aspartate-semialdehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Aspartate semialdehyde dehydrogenase | ||||||
Function / homology | ADENOSINE-2'-5'-DIPHOSPHATE / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hwang, J. / Do, H. / Lee, J.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Porphyromonas gingivalis. Authors: Hwang, J. / Do, H. / Shim, Y.S. / Lee, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.3 KB | Display | ![]() |
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PDB format | ![]() | 117.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8juoC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37299.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: aspartate semialdehyde dehydrogenase complexed with 2',5'-adenosine diphosphate. Two C-terminal residues have weak electron density map. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A1R4DY25, aspartate-semialdehyde dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.61 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→28.77 Å / Num. obs: 68236 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 16.54 Å2 / CC1/2: 1 / Net I/σ(I): 29.89 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 7.46 / Num. unique obs: 6742 / CC1/2: 0.98 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 18.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→28.77 Å
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Refine LS restraints |
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LS refinement shell |
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