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Yorodumi- PDB-5ttk: Crystal Structure of Selenomethionine-incorporated Nicotine Oxido... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ttk | |||||||||
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Title | Crystal Structure of Selenomethionine-incorporated Nicotine Oxidoreductase from Pseudomonas putida | |||||||||
Components | Amine oxidase | |||||||||
Keywords | OXIDOREDUCTASE / nicotine degradation / flavoenzyme / monoamine oxidase family / PHBH | |||||||||
Function / homology | Function and homology information nicotine dehydrogenase / nicotine catabolic process / alkaloid metabolic process / periplasmic space / oxidoreductase activity / nucleotide binding Similarity search - Function | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å | |||||||||
Authors | Tararina, M.A. / Janda, K.D. / Allen, K.N. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2016 Title: Structural Analysis Provides Mechanistic Insight into Nicotine Oxidoreductase from Pseudomonas putida. Authors: Tararina, M.A. / Janda, K.D. / Allen, K.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ttk.cif.gz | 344.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ttk.ent.gz | 292.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ttk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ttk_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5ttk_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5ttk_validation.xml.gz | 67.8 KB | Display | |
Data in CIF | 5ttk_validation.cif.gz | 89.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/5ttk ftp://data.pdbj.org/pub/pdb/validation_reports/tt/5ttk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 54134.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (strain S16) (bacteria) Strain: S16 / Gene: PPS_4081 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: F8G0P2 #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % Description: three-dimensional yellow crystals of rod-like morphology with final dimensions of 0.1 mm by 0.2 mm by 0.5 mm |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.1 M sodium citrate tribasic dihydrate pH 8.3, 15% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→48.551 Å / Num. obs: 69981 / % possible obs: 96 % / Redundancy: 5.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.193 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.51→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.88 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.51→48.551 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 23.79 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→48.551 Å
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Refine LS restraints |
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LS refinement shell |
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