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Yorodumi- PDB-4zvy: Structure of human ALDH7A1 complexed with NAD+ in space group P4212 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zvy | ||||||
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Title | Structure of human ALDH7A1 complexed with NAD+ in space group P4212 | ||||||
Components | Alpha-aminoadipic semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / aldehyde dehydrogenase / NAD / 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: 1.9 Å | ||||||
Authors | Tanner, J.J. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Structural Basis of Substrate Recognition by Aldehyde Dehydrogenase 7A1. Authors: Luo, M. / 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 | 4zvy.cif.gz | 368.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zvy.ent.gz | 298.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zvy ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zvy | HTTPS FTP |
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-Related structure data
Related structure data | 4zukC 4zulC 4zvwC 4zvxC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55620.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH7A1, ATQ1 / Production host: Escherichia coli (E. coli) References: UniProt: P49419, L-aminoadipate-semialdehyde dehydrogenase, aldehyde dehydrogenase (NAD+), betaine-aldehyde dehydrogenase #2: Chemical | ChemComp-NAD / | #3: 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: 2.27 Å3/Da / Density % sol: 45.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The reservoir contained 0.1 M Hepes pH 7.5, 0.1 M magnesium chloride hexahydrate, and 20% (w/v) PEG 3350. PH range: 7.5 |
-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: RDI CMOS_8M / Detector: CMOS / Date: Sep 24, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→53.07 Å / Num. obs: 80661 / % possible obs: 99.8 % / Redundancy: 14.6 % / Biso Wilson estimate: 24.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.028 / Net I/σ(I): 24 / Num. measured all: 1178496 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J6L Resolution: 1.9→53.07 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.23 / 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 max: 94.81 Å2 / Biso mean: 35.1148 Å2 / Biso min: 10.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→53.07 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
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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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