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- PDB-3q0e: Crystals Structure of Aspartate beta-Semialdehyde Dehydrogenase f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q0e | ||||||
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Title | Crystals Structure of Aspartate beta-Semialdehyde Dehydrogenase from Vibrio Cholerae with product of S-allyl-L-cysteine sulfoxide | ||||||
![]() | Aspartate-semialdehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Oxydoreductase / NADP | ||||||
Function / homology | ![]() aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pavlovsky, A.G. / Liu, X. / Viola, R.E. | ||||||
![]() | ![]() Title: Structural characterization of inhibitors with selectivity against members of a homologous enzyme family. Authors: Pavlovsky, A.G. / Liu, X. / Faehnle, C.R. / Potente, N. / Viola, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.7 KB | Display | ![]() |
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PDB format | ![]() | 240.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.6 KB | Display | ![]() |
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Full document | ![]() | 479.1 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 50.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pwkC ![]() 3pwsC ![]() 3pylC ![]() 3pyxC ![]() 3pzbC ![]() 3pzrC ![]() 3q11C ![]() 3q1lC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40541.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9KQG2, aspartate-semialdehyde dehydrogenase |
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-Non-polymers , 5 types, 631 molecules ![](data/chem/img/CYS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 % ammonium sulphate, 2 % PEG 400 10 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.3 Å / Num. obs: 79715 / % possible obs: 94.9 % / Redundancy: 6.2 % / Rsym value: 0.057 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.323 / % possible all: 63.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.235 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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