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Open data
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Basic information
Entry | Database: PDB / ID: 3ou6 | ||||||
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Title | DhpI-SAM complex | ||||||
![]() | SAM-dependent methyltransferase | ||||||
![]() | TRANSFERASE / O-methyltransferase / SAM | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bae, B. / Nair, S.K. | ||||||
![]() | ![]() Title: Characterization and structure of DhpI, a phosphonate O-methyltransferase involved in dehydrophos biosynthesis. Authors: Lee, J.H. / Bae, B. / Kuemin, M. / Circello, B.T. / Metcalf, W.W. / Nair, S.K. / van der Donk, W.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.2 KB | Display | ![]() |
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PDB format | ![]() | 152.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 39.8 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24605.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SAM / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.97 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M Ammonium sulphate, 100 mM Tris-HCl pH=8.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→46.47 Å / Num. all: 60586 / Num. obs: 60586 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 7.7 / Num. unique all: 6000 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.791 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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