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Yorodumi- PDB-1zum: Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zum | ||||||
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Title | Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / carboxylesterase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / NAD binding / electron transfer activity / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Larson, H.N. / Weiner, H. / Hurley, T.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Disruption of the coenzyme binding site and dimer interface revealed in the crystal structure of mitochondrial aldehyde dehydrogenase "asian" variant Authors: Larson, H.N. / Weiner, H. / Hurley, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zum.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1zum.ent.gz | 910.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/1zum ftp://data.pdbj.org/pub/pdb/validation_reports/zu/1zum | HTTPS FTP |
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-Related structure data
Related structure data | 1o05S 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 54499.695 Da / Num. of mol.: 12 / Mutation: E487K Source method: isolated from a genetically manipulated source Details: (Does Not Contain Mitochondrial Leader Sequence) / Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pT-7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P05091, aldehyde dehydrogenase (NAD+) #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GAI / #4: Chemical | ChemComp-EDO / #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: 2.416 Å3/Da / Density % sol: 47.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: ACES (N-[2-Acetamido]-2-aminoethane sulfonic acid), magnesium chloride, Guanidine HCl, PEG 6000, DTT, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: APS-1 / Detector: CCD / Date: Jun 2, 2000 / Details: APS 19ID optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42.63 Å / Num. all: 353290 / Num. obs: 345164 / % possible obs: 97.7 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 1.94 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.3 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1O05 Resolution: 2.1→42.63 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3033207.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.1276 Å2 / ksol: 0.311329 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→42.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
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Xplor file |
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