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Yorodumi- PDB-5ilo: Crystal structure of photoreceptor dehydrogenase from Drosophila ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ilo | ||||||
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Title | Crystal structure of photoreceptor dehydrogenase from Drosophila melanogaster | ||||||
Components | Photoreceptor dehydrogenase, isoform C | ||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase | ||||||
Function / homology | Function and homology information all-trans-retinol dehydrogenase (NAD+) / retinal metabolic process / all-trans-retinol dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / retinol metabolic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Hofmann, L. / Tsybovsky, Y. / Banerjee, S. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family. Authors: Hofmann, L. / Tsybovsky, Y. / Alexander, N.S. / Babino, D. / Leung, N.Y. / Montell, C. / Banerjee, S. / von Lintig, J. / Palczewski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ilo.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ilo.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ilo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ilo_validation.pdf.gz | 975.5 KB | Display | wwPDB validaton report |
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Full document | 5ilo_full_validation.pdf.gz | 982.6 KB | Display | |
Data in XML | 5ilo_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 5ilo_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/5ilo ftp://data.pdbj.org/pub/pdb/validation_reports/il/5ilo | HTTPS FTP |
-Related structure data
Related structure data | 5ilgC 1b2lS 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
#1: Protein | Mass: 29490.061 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Pdh, pcdr, CG4899, Dmel_CG4899 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7KNR7, UniProt: Q9VV42*PLUS, alcohol dehydrogenase, all-trans-retinol dehydrogenase (NAD+) #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: 2.11 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, beta- ionone |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→113.43 Å / Num. obs: 13342 / % possible obs: 98.5 % / Redundancy: 3.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.163 / Rsym value: 0.187 / Net I/av σ(I): 9.5 / Net I/σ(I): 9.53 |
Reflection shell | Resolution: 2.71→2.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.4 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B2L Resolution: 2.71→113.43 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→113.43 Å
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Refine LS restraints |
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LS refinement shell |
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