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Yorodumi- PDB-1b2l: ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS: TERNARY COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b2l | ||||||
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Title | ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS: TERNARY COMPLEX WITH NAD-CYCLOHEXANONE | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DETOXIFICATION / METABOLISM / ALCOHOL DEHYDROGENASE / DROSOPHILA LEBANONENSIS / SHORT-CHAIN DEHYDROGENASES/REDUCTASES / TERNARY COMPLEX / NAD- CYCLOHEXANONE 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 1b2l.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b2l.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 1b2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b2l_validation.pdf.gz | 487.8 KB | Display | wwPDB validaton report |
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Full document | 1b2l_full_validation.pdf.gz | 490.8 KB | Display | |
Data in XML | 1b2l_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1b2l_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b2l ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b2l | HTTPS FTP |
-Related structure data
Related structure data | 1b14C 1b15C 1b16C 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27823.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CYCLOHEXANONE / Source: (natural) Scaptodrosophila lebanonensis (fry) / References: UniProt: P10807, alcohol dehydrogenase |
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-Non-polymers , 5 types, 236 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-NDC / |
#4: Chemical | ChemComp-CYH / |
#5: Chemical | ChemComp-DTT / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8 Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 2000, 0.2 M CACL2, 0.1 M TRIS-HCL, PH= 8.0, 1MM NAD+, 1% CYCLOHEXANONE, 277 K. | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.996 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→20 Å / Num. obs: 40649 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 3 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 3 / % possible all: 91 |
Reflection | *PLUS Num. measured all: 565296 |
Reflection shell | *PLUS % possible obs: 91 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A4U Resolution: 1.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.18
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Displacement parameters | Biso mean: 11.3 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 11.3 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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