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Yorodumi- PDB-1l0c: Investigation of the Roles of Catalytic Residues in Serotonin N-A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l0c | ||||||
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Title | Investigation of the Roles of Catalytic Residues in Serotonin N-Acetyltransferase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Scheibner, K.A. / De Angelis, J. / Burley, S.K. / Cole, P.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Investigation of the roles of catalytic residues in serotonin N-acetyltransferase. Authors: Scheibner, K.A. / De Angelis, J. / Burley, S.K. / Cole, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l0c.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l0c.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 1l0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/1l0c ftp://data.pdbj.org/pub/pdb/validation_reports/l0/1l0c | HTTPS FTP |
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-Related structure data
Related structure data | 1kuvS S: Starting model for refinement |
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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: 23095.568 Da / Num. of mol.: 1 / Mutation: Y168F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) / Gene: AANAT / 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, MES pH 6.5, ammonium acetate, magnesium acetate, lithium chloride, spermidine, DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃Details: Wolf, E., (2002) J. Mol. Biol., 317, 215., 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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2000 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 7822 / Num. obs: 7188 / % possible obs: 91.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 14.1 / Num. unique all: 497 / Rsym value: 0.092 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 75910 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 93 % / Rmerge(I) obs: 0.092 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KUV Resolution: 2.3→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: 2.3→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.1877 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.193 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS |