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Yorodumi- PDB-1kuv: X-ray Crystallographic Studies of Serotonin N-acetyltransferase C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kuv | ||||||
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Title | X-ray Crystallographic Studies of Serotonin N-acetyltransferase Catalysis and Inhibition | ||||||
Components | Serotonin N-acetyltransferase | ||||||
Keywords | TRANSFERASE / Enzyme-Inhibitor Complex / Bisubstrate Analog / Alternate Conformations | ||||||
Function / homology | Function and homology information aralkylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / melatonin biosynthetic process / N-terminal protein amino acid acetylation / response to light stimulus / cellular response to cAMP / circadian rhythm / perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 | 1kuv.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kuv.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kuv_validation.pdf.gz | 481.2 KB | Display | wwPDB validaton report |
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Full document | 1kuv_full_validation.pdf.gz | 491.3 KB | Display | |
Data in XML | 1kuv_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 1kuv_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/1kuv ftp://data.pdbj.org/pub/pdb/validation_reports/ku/1kuv | 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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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-MG / |
#3: Chemical | ChemComp-CA5 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→25 Å / Num. all: 11494 / Num. obs: 10517 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 16.3 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 9.6 / Num. unique all: 1148 / Rsym value: 0.123 / % possible all: 79.5 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 25 Å / % possible obs: 92 % / Num. measured all: 86780 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 80 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Structure was solved based on MAD data collected in the vicinity of the bromine and selenium edges. Ligand density was identified by difference fourier. The final model (protein and ligand) ...Details: Structure was solved based on MAD data collected in the vicinity of the bromine and selenium edges. Ligand density was identified by difference fourier. The final model (protein and ligand) was refined at 2.0 Angstrom
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 25 Å / Num. reflection obs: 10057 / % reflection Rfree: 10 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.25 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS |