+Open data
-Basic information
Entry | Database: PDB / ID: 2j6l | ||||||
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Title | Structure of aminoadipate-semialdehyde dehydrogenase | ||||||
Components | ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1 | ||||||
Keywords | OXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / REDUCTASE / LYSINE CATABOLISM | ||||||
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 activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / 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 activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / 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: 1.3 Å | ||||||
Authors | Bunkoczi, G. / Guo, K. / Debreczeni, J.E. / Smee, C. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / von Delft, F. / Oppermann, U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Aldehyde Dehydrogenase 7A1 (Aldh7A1) is a Novel Enzyme Involved in Cellular Defense Against Hyperosmotic Stress. Authors: Brocker, C. / Lassen, N. / Estey, T. / Pappa, A. / Cantore, M. / Orlova, V.V. / Chavakis, T. / Kavanagh, K.L. / Oppermann, U. / Vasiliou, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j6l.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2j6l.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 2j6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/2j6l ftp://data.pdbj.org/pub/pdb/validation_reports/j6/2j6l | HTTPS FTP |
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-Related structure data
Related structure data | 1nzxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 54169.602 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: P49419, aldehyde dehydrogenase (NAD+) #2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-BR / #4: Chemical | ChemComp-NA / #5: 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: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | pH: 6.6 Details: 0.1 M BTPROP PH 6.6, 0.20 M NABR, 23% PEG3350, 10% ETHYLENE GLYCOLE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 12, 2006 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→49.2 Å / Num. obs: 816066 / % possible obs: 85.1 % / Observed criterion σ(I): 0 / Redundancy: 3.33 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.91 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.61 / % possible all: 44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NZX Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.345 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.057 / 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: 11.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→50 Å
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Refine LS restraints |
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