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Yorodumi- PDB-5gi6: Crystal Structure of Drosophila melanogaster Dopamine N-Acetyltra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gi6 | ||||||
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Title | Crystal Structure of Drosophila melanogaster Dopamine N-Acetyltransferase Bound to CoA and Phenylethylamine | ||||||
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: 1.65 Å | ||||||
Authors | Yang, Y.C. / Cheng, H.C. / Lyu, P.C. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of Drosophila melanogaster Dopamine N-Acetyltransferase Bound to CoA and Phenylethylamine Authors: Yang, Y.C. / 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 | 5gi6.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gi6.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 5gi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gi6_validation.pdf.gz | 775 KB | Display | wwPDB validaton report |
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Full document | 5gi6_full_validation.pdf.gz | 776.6 KB | Display | |
Data in XML | 5gi6_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 5gi6_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/5gi6 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/5gi6 | 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: 24442.049 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-265 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 | ChemComp-PEA / |
#3: Chemical | ChemComp-COA / |
#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: 2.12 Å3/Da / Density % sol: 41.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 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: Jul 29, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→30 Å / Num. obs: 26434 / % possible obs: 96.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.24 Å2 / Rmerge(I) obs: 0.048 / Net I/av σ(I): 31.628 / Net I/σ(I): 12.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→25.288 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.42 Å2 / Biso mean: 33.11 Å2 / Biso min: 15.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→25.288 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: 9
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Refinement TLS params. | Method: refined / Origin x: 1.7848 Å / Origin y: -19.1016 Å / Origin z: -8.9811 Å
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Refinement TLS group | Selection details: ALL |