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Yorodumi- PDB-8wme: Crystal Structure of Drosophila melanogaster D46A Dopamine N-Acet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wme | ||||||
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Title | Crystal Structure of Drosophila melanogaster D46A Dopamine N-Acetyltransferase | ||||||
Components | Arylalkylamine N-acetyltransferase 1 | ||||||
Keywords | TRANSFERASE / Dopamine N-acetyltransferase(Dat) / GCN5-related N-acetyltransferase(GNAT) / Arylalkylamine N-acetyltransferase(AANAT) | ||||||
Function / homology | Function and homology information chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / aralkylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / melatonin biosynthetic process / arylamine N-acetyltransferase activity / 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 / melatonin biosynthetic process / arylamine N-acetyltransferase activity / 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 / Resolution: 2.283 Å | ||||||
Authors | Wu, C.Y. / Hu, I.C. / Cheng, H.C. / Lyu, P.C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Drosophila melanogaster D46A Dopamine N-Acetyltransferase in Complex with Acetyl-CoA Authors: Wu, C.Y. / Hu, I.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 | 8wme.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wme.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 8wme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wme_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 8wme_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 8wme_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 8wme_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/8wme ftp://data.pdbj.org/pub/pdb/validation_reports/wm/8wme | HTTPS FTP |
-Related structure data
Related structure data | 8wmbC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24400.057 Da / Num. of mol.: 2 / Mutation: D46A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: speck Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q94521 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.24 Å3/Da / Density % sol: 45.19 % |
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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 HEPES, 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99984 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→30 Å / Num. obs: 18954 / % possible obs: 96.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 31.55 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.054 / Rrim(I) all: 0.128 / Χ2: 0.881 / Net I/σ(I): 13.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.283→28.776 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.32 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.67 Å2 / Biso mean: 33.8521 Å2 / Biso min: 15.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.283→28.776 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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