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Yorodumi- PDB-5gif: Crystal Structure of Drosophila melanogaster E47D Dopamine N-Acet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gif | ||||||
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Title | Crystal Structure of Drosophila melanogaster E47D Dopamine N-Acetyltransferase in Binary Complex with Acetyl-CoA | ||||||
Components | Dopamine N-acetyltransferase | ||||||
Keywords | TRANSFERASE / Dopamine N-acetyltransferase(Dat) / GCN5-related N-acetyltransferase(GNAT) / Arylalkylamine N-acetyltransferase(AANAT) / Order bi-bi sequential mechanism | ||||||
Function / homology | Function and homology information chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / aralkylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / melatonin biosynthetic process / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / dopamine catabolic process ...chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / aralkylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / melatonin biosynthetic process / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / dopamine catabolic process / sleep / N-acetyltransferase activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Yang, Y.C. / Wu, C.Y. / Cheng, H.C. / Lyu, P.C. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of Drosophila melanogaster E47D Dopamine N-Acetyltransferase in Binary Complex with Acetyl-CoA Authors: Yang, Y.C. / Wu, C.Y. / Cheng, H.C. / Lyu, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gif.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gif.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gif_validation.pdf.gz | 708.2 KB | Display | wwPDB validaton report |
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Full document | 5gif_full_validation.pdf.gz | 708.8 KB | Display | |
Data in XML | 5gif_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 5gif_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/5gif ftp://data.pdbj.org/pub/pdb/validation_reports/gi/5gif | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 24428.023 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-265 / Mutation: E47D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dat, NAT1, CG3318 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 References: UniProt: Q94521, aralkylamine N-acetyltransferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACO / | #4: 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: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1.0M NaH2PO4/1.6M K2HPO4, 0.1M Imidazole, 0.2M NaCl PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.29→30 Å / Num. obs: 53391 / % possible obs: 99 % / Redundancy: 7.4 % / Biso Wilson estimate: 12.36 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.019 / Rrim(I) all: 0.052 / Χ2: 0.987 / Net I/av σ(I): 38.63 / Net I/σ(I): 15 / Num. measured all: 397598 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→26.824 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.79 Å2 / Biso mean: 16.99 Å2 / Biso min: 7.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→26.824 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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