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Yorodumi- PDB-8wmb: Crystal Structure of Drosophila melanogaster D46A Dopamine N-Acet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wmb | ||||||
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Title | Crystal Structure of Drosophila melanogaster D46A Dopamine N-Acetyltransferase in Complex with Acetyl-CoA | ||||||
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 / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / N-acetyltransferase activity ...chitin-based cuticle sclerotization / serotonin catabolic process / octopamine catabolic process / aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / regulation of circadian sleep/wake cycle, sleep / catecholamine metabolic process / N-acetyltransferase activity / dopamine catabolic process / sleep / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.645 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 | 8wmb.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wmb.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 8wmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wmb_validation.pdf.gz | 735.3 KB | Display | wwPDB validaton report |
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Full document | 8wmb_full_validation.pdf.gz | 735.6 KB | Display | |
Data in XML | 8wmb_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 8wmb_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/8wmb ftp://data.pdbj.org/pub/pdb/validation_reports/wm/8wmb | HTTPS FTP |
-Related structure data
Related structure data | 8wmeC 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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Unit cell |
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-Components
#1: Protein | Mass: 24400.057 Da / Num. of mol.: 1 / 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 |
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#2: Chemical | ChemComp-ACO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M NaH2PO4, 1.6M K2HPO4, 0.1M Imidazole, 0.2M NaCl PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.64→30 Å / Num. obs: 46902 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.04 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Χ2: 1.07 / Net I/σ(I): 21.82 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.645→22.744 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5172 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.645→22.744 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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