[English] 日本語
Yorodumi- PDB-2onn: Arg475Gln Mutant of Human Mitochondrial Aldehyde Dehydrogenase, A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2onn | ||||||
---|---|---|---|---|---|---|---|
Title | Arg475Gln Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Apo form | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ALDH / NAD / Rossmann Fold | ||||||
Function / homology | Function and homology information Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / 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 / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / mitochondrion / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2onn.cif.gz | 737 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2onn.ent.gz | 616.3 KB | Display | PDB format |
PDBx/mmJSON format | 2onn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2onn_validation.pdf.gz | 487.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2onn_full_validation.pdf.gz | 536.1 KB | Display | |
Data in XML | 2onn_validation.xml.gz | 138.2 KB | Display | |
Data in CIF | 2onn_validation.cif.gz | 190 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/2onn ftp://data.pdbj.org/pub/pdb/validation_reports/on/2onn | HTTPS FTP |
-Related structure data
Related structure data | 2onmC 2onoC 2onpC 1o05S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.6 Details: 100 mM ACES (N-[2-Acetamido]-2-aminoethane sufonic acid), 10mM MgCl2, 100 mM Guanidine HCl, 16% w/v PEG 6000, 4 mM DTT, pH 6.6, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 12, 1999 |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→99 Å / Num. all: 99123 / Num. obs: 95356 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.75→2.84 Å / Rmerge(I) obs: 0.298 / % possible all: 82 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O05 Resolution: 2.75→37.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4648163.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.27171 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→37.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|