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Yorodumi- PDB-2ono: Arg475Gln Mutant of Mitochondrial Aldehyde Dehydrogenase, apo for... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ono | ||||||
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Title | Arg475Gln Mutant of Mitochondrial Aldehyde Dehydrogenase, apo form, pseudo-merohedrally twinned | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ALDH / NAD / 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Larson, H.N. / Hurley, T.D. | ||||||
Citation | 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 | 2ono.cif.gz | 744.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ono.ent.gz | 617.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ono.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/2ono ftp://data.pdbj.org/pub/pdb/validation_reports/on/2ono | HTTPS FTP |
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-Related structure data
Related structure data | 2onmC 2onnC 2onpC 1o05S 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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1 |
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2 |
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Unit cell |
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Details | The biological unit is a tetramer. There are 3 biological untils in the assymmetric unit. The biological unit 1 consists of chain(s) A, B, C, D. The biological unit 2 consists of chain(s) E, F, G, H. |
-Components
#1: Protein | Mass: 54470.562 Da / Num. of mol.: 8 / Mutation: R475Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pT-7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+) #2: 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: 2.069 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 293 K / pH: 6.6 Details: 100 mM ACES (N-[2-Acetamido]-2-aminoethane sufonic acid), 5 mM MgCl2, 100 mM Guanidine HCl, 18% w/v PEG 6000, 6 mM DTT, pH 6.6, vapor diffusion, temperature 293K, pH 6.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 3, 2003 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→25 Å / Num. obs: 186854 / % possible obs: 97.5 % / Observed criterion σ(I): 0.2 / Biso Wilson estimate: 21.84 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.198 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O05 Resolution: 2.15→10 Å / Num. parameters: 125536 / Num. restraintsaints: 316424 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 31383 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→10 Å
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Refine LS restraints |
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