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Yorodumi- PDB-3n81: T244A mutant of Human mitochondrial aldehyde dehydrogenase, apo form -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n81 | ||||||
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Title | T244A mutant of Human mitochondrial aldehyde dehydrogenase, apo form | ||||||
Components | Aldehyde dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / ALDH / Rossmann fold | ||||||
Function / homology | Function and homology information Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / alcohol metabolic process / phenylacetaldehyde dehydrogenase activity / 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 / aldehyde catabolic process / alcohol metabolic process / phenylacetaldehyde dehydrogenase activity / 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 / Direct Refinement / Resolution: 1.7 Å | ||||||
Authors | Gonzalez-Segura, L. / Hurley, T.D. | ||||||
Citation | Journal: To be published Title: Conformational Selection During Catalysis: The role of Threonine 244 in ALDH2 Authors: Ho, K.-K. / Gonzalez-Segura, L. / Perez-Miller, S. / Weiner, H. / Hurley, T.D. #1: Journal: Biochemistry / Year: 2006 Title: Selective Alteration of the Rate-Limiting Step in Cytosolic Aldehyde Dehydrogenase through Random Mutagenesis Authors: Ho, K.-K. / Hurley, T.D. / Weiner, H. #2: Journal: J. Biol. Chem. / Year: 2007 Title: Structural and Functional Consequences of Coenzyme Binding to the Inactive Asian Variant of Mitochondrial Aldehyde Dehydrogenase (ROLES OF RESIDUES 475 AND 487) Authors: Larson, H.N. / Zhou, J. / Chen, Z. / Stamler, J.S. / 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 | 3n81.cif.gz | 827.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n81.ent.gz | 682.2 KB | Display | PDB format |
PDBx/mmJSON format | 3n81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/3n81 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/3n81 | HTTPS FTP |
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-Related structure data
Related structure data | 3n80C 3n82C 3n83C 1o05S 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
#1: Protein | Mass: 54469.602 Da / Num. of mol.: 8 / Fragment: Mature sequence, residues 18-517 / Mutation: T244A Source method: isolated from a genetically manipulated source Details: lacks mitochondrial leader sequence / Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pT-7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 6.4 Details: 100 MM ACES (N-[2-ACETAMIDO]-2-AMINOETHANE SULFONIC ACID), 1-10MM MGCL2, 100-200 MM GUANIDINE HCL, 16-17% W/V PEG 6000, pH 6.4, vapor diffusion, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2007 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 416273 / % possible obs: 99.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.4 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: Direct Refinement Starting model: PDB Entry 1o05 Resolution: 1.7→42.07 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.288 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 57.42 Å2 / Biso mean: 18.142 Å2 / Biso min: 4.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→42.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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