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Yorodumi- PDB-6o4d: Structure of ALDH7A1 mutant W175A complexed with L-pipecolic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o4d | ||||||
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Title | Structure of ALDH7A1 mutant W175A complexed with L-pipecolic acid | ||||||
Components | (Alpha-aminoadipic semialdehyde ...) x 3 | ||||||
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 (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 / FOURIER SYNTHESIS / Resolution: 1.88 Å | ||||||
Authors | Tanner, J.J. / Korasick, D.A. / Laciak, A.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Febs J. / Year: 2020 Title: Structural and biochemical consequences of pyridoxine-dependent epilepsy mutations that target the aldehyde binding site of aldehyde dehydrogenase ALDH7A1. Authors: Laciak, A.R. / Korasick, D.A. / Wyatt, J.W. / Gates, K.S. / 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 | 6o4d.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6o4d.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6o4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o4d_validation.pdf.gz | 554.7 KB | Display | wwPDB validaton report |
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Full document | 6o4d_full_validation.pdf.gz | 587.7 KB | Display | |
Data in XML | 6o4d_validation.xml.gz | 155.9 KB | Display | |
Data in CIF | 6o4d_validation.cif.gz | 218.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/6o4d ftp://data.pdbj.org/pub/pdb/validation_reports/o4/6o4d | HTTPS FTP |
-Related structure data
Related structure data | 6o4bC 6o4cC 6o4eC 6o4fC 6o4gC 6o4hC 4zulS S: Starting model for refinement C: citing same article (ref.) |
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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
-Alpha-aminoadipic semialdehyde ... , 3 types, 8 molecules ABGCDEFH
#1: Protein | Mass: 55521.238 Da / Num. of mol.: 1 / Mutation: W175A 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 | ||
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#2: Protein | Mass: 55553.238 Da / Num. of mol.: 2 / Mutation: W175A 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 #3: Protein | Mass: 55505.238 Da / Num. of mol.: 5 / Mutation: W175A 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 |
-Non-polymers , 7 types, 2078 molecules
#4: Chemical | ChemComp-6PC / #5: Chemical | ChemComp-PGE / #6: Chemical | #7: Chemical | ChemComp-1PE / | #8: Chemical | ChemComp-PG4 / #9: Chemical | ChemComp-EDO / | #10: 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: 2.25 Å3/Da / Density % sol: 45.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.1 M MgCl2, 0.1 M Tris pH 7.2, 0.1 M sodium acetate trihydrate, 20% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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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: Apr 3, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.88→62.9 Å / Num. obs: 316551 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Net I/σ(I): 14 / Num. measured all: 1137039 / Scaling rejects: 55 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4zul Resolution: 1.88→57.962 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 22.83 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→57.962 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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