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Yorodumi- PDB-1o01: Human mitochondrial aldehyde dehydrogenase complexed with crotona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o01 | ||||||
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Title | Human mitochondrial aldehyde dehydrogenase complexed with crotonaldehyde, NAD(H) and Mg2+ | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ALDH / NAD / NADH / isomerization | ||||||
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 | Perez-Miller, S.J. / Hurley, T.D. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Coenzyme isomerization is integral to catalysis in aldehyde dehydrogenase Authors: Perez-Miller, S.J. / 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 | 1o01.cif.gz | 833.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o01.ent.gz | 684.6 KB | Display | PDB format |
PDBx/mmJSON format | 1o01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/1o01 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/1o01 | HTTPS FTP |
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-Related structure data
Related structure data | 1nzwC 1nzxC 1nzzC 1o00C 1o02C 1o04C 1cw3S 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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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 54499.629 Da / Num. of mol.: 8 Fragment: Complete mature sequence (does not contain mitochondrial leader sequence). Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2 OR ALDM / Plasmid: PET7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P05091, aldehyde dehydrogenase (NAD+) |
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-Non-polymers , 7 types, 3711 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-GAI / #5: Chemical | ChemComp-NAD / #6: Chemical | ChemComp-CRD / ( #7: Chemical | ChemComp-EDO / #8: 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: 1.95 Å3/Da / Density % sol: 36.57 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: ACES, PEG 6000, Guanidine HCl, MgCl2, DTT, NAD+. Crystal soaked with crotonaldehyde prior to data collection., pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6.6 / PH range high: 6.2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9786 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Aug 29, 1999 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→35 Å / Num. all: 207332 / Num. obs: 188672 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 7.2 / Num. unique all: 14801 / % possible all: 72 |
Reflection | *PLUS Lowest resolution: 45 Å / % possible obs: 90.7 % / Num. measured all: 688308 |
Reflection shell | *PLUS % possible obs: 71.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CW3 Resolution: 2.15→34.84 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 6380979.5 / Data cutoff high rms absF: 6380979.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using amplitudes
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.2129 Å2 / ksol: 0.310269 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→34.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 45 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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