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Yorodumi- PDB-7cix: Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cix | ||||||
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Title | Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with CoA | ||||||
Components | Agmatine N-acetyltransferase | ||||||
Keywords | TRANSFERASE / GCN5-related N-acetyltransferase(GNAT) / Arylalkylamine N-acetyltransferase(AANAT) | ||||||
Function / homology | Function and homology information arylamine N-acetyltransferase / aralkylamine N-acetyltransferase activity / arylamine N-acetyltransferase activity / N-acetyltransferase activity Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.748 Å | ||||||
Authors | Chen, J.J. / Hu, I.C. / Wu, C.Y. / Lyu, P.C. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with CoA Authors: Chen, J.J. / Hu, I.C. / Wu, C.Y. / Lyu, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cix.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cix.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/7cix ftp://data.pdbj.org/pub/pdb/validation_reports/ci/7cix | HTTPS FTP |
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-Related structure data
Related structure data | 5k9nS 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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-Components
#1: Protein | Mass: 23783.109 Da / Num. of mol.: 1 / Mutation: S171A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: AgmNAT, AANATL8, Dmel\CG15766, CG15766, Dmel_CG15766 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9W469, arylamine N-acetyltransferase |
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#2: Chemical | ChemComp-COA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium HEPES (pH7.0), 2.1M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.748→30 Å / Num. obs: 19454 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Χ2: 1.033 / Net I/σ(I): 25.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5k9n Resolution: 1.748→25.899 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.57 / 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: 69.26 Å2 / Biso mean: 27.4226 Å2 / Biso min: 14.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.748→25.899 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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