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Yorodumi- PDB-1kuy: X-ray Crystallographic Studies of Serotonin N-acetyltransferase C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kuy | ||||||
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Title | X-ray Crystallographic Studies of Serotonin N-acetyltransferase Catalysis and Inhibition | ||||||
Components | Serotonin N-acetyltransferaseAralkylamine N-acetyltransferase | ||||||
Keywords | TRANSFERASE / Enzyme-Inhibitor Complex / Bisubstrate Analog / Alternate Conformations | ||||||
Function / homology | Function and homology information aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / N-terminal protein amino acid acetylation / cellular response to cAMP / circadian rhythm / perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wolf, E. / De Angelis, J. / Khalil, E.M. / Cole, P.A. / Burley, S.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: X-ray crystallographic studies of serotonin N-acetyltransferase catalysis and inhibition. Authors: Wolf, E. / De Angelis, J. / Khalil, E.M. / Cole, P.A. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kuy.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kuy.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kuy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/1kuy ftp://data.pdbj.org/pub/pdb/validation_reports/ku/1kuy | HTTPS FTP |
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-Related structure data
Related structure data | 1kuvSC 1kuxC 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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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 23111.568 Da / Num. of mol.: 1 / Mutation: MET substituted by Se-met Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) / Gene: U29663 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q29495, aralkylamine N-acetyltransferase |
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#2: Chemical | ChemComp-COT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 2000, MPD, ammonium sulfate, MES pH 6.5, magnesium acetate, DTT, spermidine, and lithium chloride. VAPOR DIFFUSION, HANGING DROP at 277K, temperature 277.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 9, 2000 / Details: Yale mirrors |
Radiation | Monochromator: Coated Yale mirrors, 0.00015" Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 6689 / Num. obs: 6248 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 12.3 / Num. unique all: 650 / Rsym value: 0.133 / % possible all: 94.2 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 94.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KUV Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Structure was refined with waters and ligand was modeled based on difference fourier electron density. Ligand was included in final refinement
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.203 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 |