+Open data
-Basic information
Entry | Database: PDB / ID: 5xyk | ||||||
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Title | Structure of Transferase | ||||||
Components | Putative cytoplasmic proteinCytoplasm | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | ARGININE / : / URIDINE-5'-DIPHOSPHATE / Putative cytoplasmic protein Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Park, J.B. / Yoo, Y. / Kim, J. / Cho, H.S. | ||||||
Citation | Journal: To Be Published Title: Structure of Transferase Authors: Park, J.B. / Yoo, Y. / Kim, J. / Cho, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xyk.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xyk.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xyk ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xyk | HTTPS FTP |
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-Related structure data
Related structure data | 5h5yS 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: 39616.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain 4/74) (bacteria) Strain: 4/74 / Gene: STM474_2223 / Production host: Escherichia coli (E. coli) / References: UniProt: E8XCX6 |
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#2: Chemical | ChemComp-ARG / |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-UDP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.05 % |
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Crystal grow | Temperature: 290 K / Method: evaporation, recrystallization / pH: 5.5 Details: 0.2M ammonium acetate 0.1M Bis-Tris pH5.5 25% PEG2250 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→67.08 Å / Num. obs: 9052 / % possible obs: 94.87 % / Redundancy: 7.6 % / Net I/σ(I): 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H5Y Resolution: 2.57→67.08 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.822 / SU B: 14.817 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.524 Å2
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Refinement step | Cycle: 1 / Resolution: 2.57→67.08 Å
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Refine LS restraints |
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