+Open data
-Basic information
Entry | Database: PDB / ID: 1ag8 | ||||||
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Title | ALDEHYDE DEHYDROGENASE FROM BOVINE MITOCHONDRIA | ||||||
Components | ALDEHYDE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ALCOHOL METABOLISM / ALDEHYDE OXIDATION / ALPHA/BETA DOMAIN / DEHYDROGENASE | ||||||
Function / homology | Function and homology information Metabolism of serotonin / Ethanol oxidation / Smooth Muscle Contraction / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / ethanol catabolic process / carboxylesterase activity ...Metabolism of serotonin / Ethanol oxidation / Smooth Muscle Contraction / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / ethanol catabolic process / carboxylesterase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Mitochondrial protein degradation / NAD binding / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.65 Å | ||||||
Authors | Steinmetz, C.G. / Hurley, T.D. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Structure of mitochondrial aldehyde dehydrogenase: the genetic component of ethanol aversion. Authors: Steinmetz, C.G. / Xie, P. / Weiner, H. / 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 | 1ag8.cif.gz | 364.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ag8.ent.gz | 310.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ag8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ag8_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 1ag8_full_validation.pdf.gz | 494.2 KB | Display | |
Data in XML | 1ag8_validation.xml.gz | 68.5 KB | Display | |
Data in CIF | 1ag8_validation.cif.gz | 94 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1ag8 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1ag8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
#1: Protein | Mass: 54494.715 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE / Source: (natural) Bos taurus (cattle) / Cellular location: MITOCHONDRIA / Organ: LIVER / Organelle: MITOCHONDRIA / References: UniProt: P20000, aldehyde dehydrogenase (NAD+) #2: 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: 2.53 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 14% PEG 8000, 100 MM MES, PH 6.5, 0.2 MM MGCL2, 1MM NAD; THEN SOAKED IN SAME SOLUTION WITHOUT NAD OR MGCL2 FOR 1 WEEK. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→48 Å / Num. obs: 55485 / % possible obs: 83 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.64→2.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.5 / % possible all: 59 |
Reflection | *PLUS Num. measured all: 213121 |
Reflection shell | *PLUS % possible obs: 59 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.65→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 14.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→8 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.65→2.77 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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