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Yorodumi- PDB-4fqf: Crystal structure of a thionitrate intermediate of human aldehyde... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fqf | ||||||
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Title | Crystal structure of a thionitrate intermediate of human aldehyde dehydrogenase-2 | ||||||
Components | Aldehyde dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / aldehydes / esters / organic nitrates / NAD / oxidoreductase-intermediate complex | ||||||
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: 2.281 Å | ||||||
Authors | Lang, B.S. / Gruber, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Vascular Bioactivation of Nitroglycerin by Aldehyde Dehydrogenase-2: REACTION INTERMEDIATES REVEALED BY CRYSTALLOGRAPHY AND MASS SPECTROMETRY. Authors: Lang, B.S. / Gorren, A.C. / Oberdorfer, G. / Wenzl, M.V. / Furdui, C.M. / Poole, L.B. / Mayer, B. / Gruber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fqf.cif.gz | 403.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fqf.ent.gz | 329 KB | Display | PDB format |
PDBx/mmJSON format | 4fqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/4fqf ftp://data.pdbj.org/pub/pdb/validation_reports/fq/4fqf | HTTPS FTP |
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-Related structure data
Related structure data | 4fr8C 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 54499.629 Da / Num. of mol.: 4 / Fragment: unp residues 18-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Production host: Escherichia coli (E. coli) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+) |
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-Non-polymers , 6 types, 911 molecules
#2: Chemical | ChemComp-2NO / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-URE / #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | NITROGEN DIOXIDE IS COVALENTLY |
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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: 2.05 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 100 mM bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (Bis-TRIS), 25% PEG 3350, 60 mM urea; 13.3 mM magnesium chloride, 8.9 mM tris(2-carboxyethyl)phosphine (TCEP), 4.4 mM NAD+, 45.8 mM ...Details: 100 mM bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (Bis-TRIS), 25% PEG 3350, 60 mM urea; 13.3 mM magnesium chloride, 8.9 mM tris(2-carboxyethyl)phosphine (TCEP), 4.4 mM NAD+, 45.8 mM glucose, crystals have been soaked with glyceryl trinitrate (GTN), pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 30, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 2.281→19.83 Å / Num. all: 521666 / Num. obs: 81819 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.28→2.39 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.295 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1o05 Resolution: 2.281→19.802 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 19.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.328 Å2 / ksol: 0.442 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.281→19.802 Å
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Refine LS restraints |
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LS refinement shell |
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