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Yorodumi- PDB-7dak: The crystal structure of a serotonin N-acetyltransferase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dak | ||||||
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Title | The crystal structure of a serotonin N-acetyltransferase in complex with 5-Methoxytryptamine and acetyl-CoA from Oryza Sativa | ||||||
Components | Serotonin N-acetyltransferase 1, chloroplastic | ||||||
Keywords | TRANSFERASE / N-acetyltransferase | ||||||
Function / homology | Function and homology information transport of virus in multicellular host / mucilage biosynthetic process involved in seed coat development / photosynthetic state transition / seed oilbody biogenesis / regulation of starch metabolic process / response to mannitol / regulation of anthocyanin metabolic process / negative regulation of seed germination / aralkylamine N-acetyltransferase / regulation of photoperiodism, flowering ...transport of virus in multicellular host / mucilage biosynthetic process involved in seed coat development / photosynthetic state transition / seed oilbody biogenesis / regulation of starch metabolic process / response to mannitol / regulation of anthocyanin metabolic process / negative regulation of seed germination / aralkylamine N-acetyltransferase / regulation of photoperiodism, flowering / aralkylamine N-acetyltransferase activity / thylakoid membrane organization / melatonin biosynthetic process / regulation of stomatal closure / response to high light intensity / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / response to hydrogen sulfide / serotonin metabolic process / N-acetyltransferase activity / response to osmotic stress / protein quality control for misfolded or incompletely synthesized proteins / defense response to fungus / response to cold / chloroplast / circadian rhythm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zhou, Y.Z. / Liao, L.J. / Tang, T. / Guo, Y. / Liu, X.K. / Liu, B. / Zhao, Y.C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Structural and Molecular Dynamics Analysis of Plant Serotonin N-Acetyltransferase Reveal an Acid/Base-Assisted Catalysis in Melatonin Biosynthesis. Authors: Liao, L. / Zhou, Y. / Xu, Y. / Zhang, Y. / Liu, X. / Liu, B. / Chen, X. / Guo, Y. / Zeng, Z. / Zhao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dak.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dak.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 7dak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dak_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7dak_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7dak_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7dak_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7dak ftp://data.pdbj.org/pub/pdb/validation_reports/da/7dak | HTTPS FTP |
-Related structure data
Related structure data | 6k5mC 7daiC 7dajC 7dalC 6iv7S S: Starting model for refinement C: citing same article (ref.) |
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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: 18507.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: SNAT1, GNAT5, NSI, SNAT, Os05g0481000, LOC_Os05g40260, OsJ_018182, OsJ_18949, OSJNBa0095J22.4 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5KQI6, aralkylamine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.5 Å3/Da / Density % sol: 55.76 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% (w/v) Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→19.65 Å / Num. obs: 9575 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 49.07 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.036 / Rrim(I) all: 0.129 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1360 / Rpim(I) all: 0.238 / Rrim(I) all: 0.636 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IV7 Resolution: 2.8→19.65 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.35 / 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: 91.54 Å2 / Biso mean: 46.8089 Å2 / Biso min: 18.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→19.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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