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Yorodumi- PDB-6k5m: The crystal structure of a serotonin N-acetyltransferase from Ory... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k5m | ||||||
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Title | The crystal structure of a serotonin N-acetyltransferase from Oryza Sativa (Rice) | ||||||
Components | Serotonin N-acetyltransferase 1, chloroplastic | ||||||
Keywords | TRANSFERASE / serotonin 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 / SAD / Resolution: 1.793 Å | ||||||
Authors | Zhou, Y.Z. / Liao, L.J. / Liu, X.K. / Guo, Y. / Zhao, Y.C. / Zeng, Z.X. | ||||||
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 | 6k5m.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k5m.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 6k5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k5m_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 6k5m_full_validation.pdf.gz | 437.6 KB | Display | |
Data in XML | 6k5m_validation.xml.gz | 9 KB | Display | |
Data in CIF | 6k5m_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/6k5m ftp://data.pdbj.org/pub/pdb/validation_reports/k5/6k5m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19514.594 Da / Num. of mol.: 1 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) / Strain (production host): BL21(DE3) References: UniProt: Q5KQI6, aralkylamine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: 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: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion / Details: 2M MgCl2, 18% PEG8000, Tris-HCl, PH8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2017 |
Radiation | Monochromator: Se / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 18235 / % possible obs: 100 % / Redundancy: 24.9 % / Biso Wilson estimate: 35.14 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 67.435 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 26.3 % / Rmerge(I) obs: 0.857 / Num. unique obs: 1781 / CC1/2: 0.903 / Rsym value: 0.857 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.793→41.058 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.74 Å2 / Biso mean: 40.8758 Å2 / Biso min: 20.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.793→41.058 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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