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Yorodumi- PDB-1ad3: CLASS 3 ALDEHYDE DEHYDROGENASE COMPLEX WITH NICOTINAMIDE-ADENINE-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ad3 | ||||||
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Title | CLASS 3 ALDEHYDE DEHYDROGENASE COMPLEX WITH NICOTINAMIDE-ADENINE-DINUCLEOTIDE | ||||||
Components | ALDEHYDE DEHYDROGENASE (CLASS 3) | ||||||
Keywords | OXIDOREDUCTASE / NADP / AROMATIC ALDEHYDE | ||||||
Function / homology | Function and homology information aldehyde dehydrogenase [NAD(P)+] / Phase I - Functionalization of compounds / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / : / cellular aldehyde metabolic process / response to xenobiotic stimulus => GO:0009410 / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / : ...aldehyde dehydrogenase [NAD(P)+] / Phase I - Functionalization of compounds / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / : / cellular aldehyde metabolic process / response to xenobiotic stimulus => GO:0009410 / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / : / aldehyde dehydrogenase (NAD+) activity / response to nutrient / response to glucocorticoid / response to cAMP / response to organic cyclic compound / membrane => GO:0016020 / response to hypoxia / positive regulation of cell population proliferation / endoplasmic reticulum / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / ISIRAS / Resolution: 2.6 Å | ||||||
Authors | Liu, Z.-J. / Rose, J. / Wang, B.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann fold. Authors: Liu, Z.J. / Sun, Y.J. / Rose, J. / Chung, Y.J. / Hsiao, C.D. / Chang, W.R. / Kuo, I. / Perozich, J. / Lindahl, R. / Hempel, J. / Wang, B.C. #1: Journal: Enzymology and Molecular Biology of Carbonyl Metabolism 6 (in: Adv.Exp. Med.Biol., V.414) Year: 1997 Title: Crystal Structure of a Class 3 Aldehyde Dehydrogenase at 2.6 Angstroms Resolution Authors: Liu, Z.-J. / Hempel, J. / Sun, J. / Rose, J. / Hsiao, D. / Chang, W.-R. / Chung, Y.-J. / Kuo, I. / Lindahl, R. / Wang, B.-C. #2: Journal: Enzymology and Molecular Biology of Carbonyl Metabolism 6 (in: Adv.Exp. Med.Biol., V.414) Year: 1997 Title: Conserved Residues in the Aldehyde Dehydrogenase Family Authors: Hempel, J. / Liu, Z.-J. / Perozich, J. / Rose, J. / Lindahl, R. / Wang, B.-C. #3: Journal: Proteins / Year: 1990 Title: Preliminary Crystallographic Analysis of Class 3 Rat Liver Aldehyde Dehydrogenase Authors: Rose, J.P. / Hempel, J. / Kuo, I. / Lindahl, R. / Wang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ad3.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ad3.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ad3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ad3_validation.pdf.gz | 537.3 KB | Display | wwPDB validaton report |
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Full document | 1ad3_full_validation.pdf.gz | 561.2 KB | Display | |
Data in XML | 1ad3_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 1ad3_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/1ad3 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/1ad3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.1895, 0.0654, -0.9797), Vector: Details | ALDEHYDE DEHYDROGENASE IS A HOMODIMER. THE FULL DIMER IS PRESENT IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. | |
-Components
#1: Protein | Mass: 50313.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PTA1DH / Production host: Escherichia coli (E. coli) / Strain (production host): BH101 References: UniProt: P11883, aldehyde dehydrogenase [NAD(P)+] #2: Chemical | #3: 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: 2.45 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: Rose, J.P., (1990) Proteins: Struct.,Funct., Genet., 8, 305. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1994 / Details: SUPPER MIRRORS (SMALL) |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 25656 / % possible obs: 80 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 23.62 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.444 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.29 / % possible all: 50 |
Reflection shell | *PLUS % possible obs: 50 % |
-Processing
Software |
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Refinement | Method to determine structure: ISIRAS / Resolution: 2.6→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 18.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.7 Å / Rfactor Rfree error: 0.031
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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