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Yorodumi- PDB-1o04: Cys302Ser mutant of human mitochondrial aldehyde dehydrogenase co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o04 | ||||||
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Title | Cys302Ser mutant of human mitochondrial aldehyde dehydrogenase complexed with NAD+ and Mg2+ | ||||||
Components | Aldehyde dehydrogenase, mitochondrial precursor | ||||||
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 / 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: 1.42 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 | 1o04.cif.gz | 877.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o04.ent.gz | 715.9 KB | Display | PDB format |
PDBx/mmJSON format | 1o04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/1o04 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/1o04 | HTTPS FTP |
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-Related structure data
Related structure data | 1nzwC 1nzxC 1nzzC 1o00C 1o01C 1o02C 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: 54483.566 Da / Num. of mol.: 8 Fragment: Complete mature sequence (does not contain mitochondrial leader sequence). Mutation: C302S 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 , 6 types, 5099 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-GAI / #6: Chemical | ChemComp-EDO / #7: 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: 1.88 Å3/Da / Density % sol: 34.21 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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., 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: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 1, 2001 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→50 Å / Num. all: 713549 / Num. obs: 683580 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.42→1.47 Å / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.8 / Num. unique all: 52512 / % possible all: 74 |
Reflection | *PLUS Num. measured all: 3220059 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 74 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CW3 Resolution: 1.42→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.942 / SU ML: 0.036 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: Engh & Huber / Details: MLKF refinement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.891 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.42→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.457 Å / Total num. of bins used: 20
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.171 / Rfactor Rwork: 0.145 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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