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- PDB-6pd1: PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pd1 | ||||||
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Title | PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransferase and 2-aminoethylphosphonate (AEP) transaminase from Treponema denticola | ||||||
![]() | Nucleotidyl transferase/aminotransferase, class V | ||||||
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Function / homology | ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suits, M.D.L. / Whiteside, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. Authors: Rice, K. / Batul, K. / Whiteside, J. / Kelso, J. / Papinski, M. / Schmidt, E. / Pratasouskaya, A. / Wang, D. / Sullivan, R. / Bartlett, C. / Weadge, J.T. / Van der Kamp, M.W. / Moreno- ...Authors: Rice, K. / Batul, K. / Whiteside, J. / Kelso, J. / Papinski, M. / Schmidt, E. / Pratasouskaya, A. / Wang, D. / Sullivan, R. / Bartlett, C. / Weadge, J.T. / Van der Kamp, M.W. / Moreno-Hagelsieb, G. / Suits, M.D. / Horsman, G.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 482.5 KB | Display | ![]() |
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PDB format | ![]() | 392.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pd2C ![]() 1jykS ![]() 1vjoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 70148.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 35405 / CIP 103919 / DSM 14222 / Gene: TDE_1415 / Production host: ![]() ![]() ![]() |
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-Non-polymers , 6 types, 195 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ChemComp-GOL / | ![]() #6: Chemical | ChemComp-NI / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.7 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.01 M nickel II chloride hexahydrate, 0.1 M Tris-HCl, pH 8.5, 1.0 M lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.72→38 Å / Num. obs: 82344 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.996 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.72→2.77 Å / Num. unique obs: 4114 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1JYK, 1VJO Resolution: 2.72→38 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→38 Å
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Refine LS restraints |
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LS refinement shell |
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