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Yorodumi- PDB-1b15: ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b15 | ||||||
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Title | ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-ACETONE | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DETOXIFICATION / METABOLISM / ALCOHOL DEHYDROGENASE / DROSOPHILA LEBANONENSIS / SHORT-CHAIN DEHYDROGENASES/REDUCTASES / TERNARY COMPLEX / NAD- ACETONE ADDUCT | ||||||
Function / homology | Function and homology information alcohol metabolic process / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Scaptodrosophila lebanonensis (fry) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Benach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: observation of an enzyme-bound NAD-ketone adduct at 1.4 A resolution by X-ray crystallography. Authors: Benach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R. #1: Journal: J.Mol.Biol. / Year: 1998 Title: The Refined Crystal Structure of Drosophila Lebanonensis Alcohol Dehydrogenase at 1.9 A Resolution Authors: Benach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b15.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b15.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b15_validation.pdf.gz | 521.4 KB | Display | wwPDB validaton report |
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Full document | 1b15_full_validation.pdf.gz | 534.3 KB | Display | |
Data in XML | 1b15_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1b15_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/1b15 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/1b15 | HTTPS FTP |
-Related structure data
Related structure data | 1b14C 1b16C 1b2lC 1a4uS C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.982541, -0.172445, 0.06983), Vector: |
-Components
#1: Protein | Mass: 27823.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NAD-ACETONE / Source: (natural) Scaptodrosophila lebanonensis (fry) / References: UniProt: P10807, alcohol dehydrogenase #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: 2.15 Å3/Da / Density % sol: 45.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 28% PEG 2000, 0.2 M CACL2, 0.1 M TRIS-HCL, PH=7.5, 1MM NAD+, 1% ACETONE, 277 K. | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 8.6 / Method: vapor diffusion, sitting drop / Details: Ladenstein, R., (1995) Acta Crystallog., D51, 69. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→99 Å / Num. obs: 25664 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2.16→2.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.27 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 108862 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A4U Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 24.9 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.198 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.9 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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