+Open data
-Basic information
Entry | Database: PDB / ID: 4x0u | ||||||
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Title | Structure ALDH7A1 inactivated by 4-diethylaminobenzaldehyde | ||||||
Components | Alpha-aminoadipic semialdehyde dehydrogenase | ||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / ALDEHYDE DEHYDROGENASE / NAD / OXIDOREDUCTASE / LYSINE CATABOLISM / oxidoreductase-oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) activity / Lysine catabolism / cellular aldehyde metabolic process / glycine betaine biosynthetic process from choline / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) activity / Lysine catabolism / cellular aldehyde metabolic process / glycine betaine biosynthetic process from choline / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / sensory perception of sound / mitochondrial matrix / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Luo, M. / Tanner, J.J. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Diethylaminobenzaldehyde Is a Covalent, Irreversible Inactivator of ALDH7A1. Authors: Luo, M. / Gates, K.S. / Henzl, M.T. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x0u.cif.gz | 728.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x0u.ent.gz | 603.7 KB | Display | PDB format |
PDBx/mmJSON format | 4x0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x0u_validation.pdf.gz | 477.1 KB | Display | wwPDB validaton report |
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Full document | 4x0u_full_validation.pdf.gz | 485.7 KB | Display | |
Data in XML | 4x0u_validation.xml.gz | 66.5 KB | Display | |
Data in CIF | 4x0u_validation.cif.gz | 94.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/4x0u ftp://data.pdbj.org/pub/pdb/validation_reports/x0/4x0u | HTTPS FTP |
-Related structure data
Related structure data | 4x0tC 2j6lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | tetramer |
-Components
#1: Protein | Mass: 55620.367 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Cys302 is covalently modified by the attachment of 4-diethylaminobenzaldehyde in a thioacyl linkage. Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH7A1, ATQ1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P49419, L-aminoadipate-semialdehyde dehydrogenase, aldehyde dehydrogenase (NAD+), betaine-aldehyde dehydrogenase #2: Chemical | ChemComp-3W9 / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Reservoir contained 0.2 M MgCl2, 25% (w/v) PEG3350, 0.1 M Tris at pH of 8.2, 1% DMSO, 200 micromolar 4-diethylaminobenzaldehyde. Protein stock solution contained 3 mg/mL ALDH7A1 and 200 micromolar DEAB. PH range: 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: CUSTOM-MADE / Detector: CMOS / Date: Nov 16, 2013 / Details: Taurus-1 detector |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→51.49 Å / Num. obs: 148899 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 25.57 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J6L Resolution: 1.95→51.49 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.89 / 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 mean: 33.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→51.49 Å
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Refine LS restraints |
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LS refinement shell |
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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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