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Open data
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Basic information
Entry | Database: PDB / ID: 3tfi | ||||||
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Title | DMSP-dependent demethylase from P. ubique - with substrate DMSP | ||||||
![]() | GcvT-like Aminomethyltransferase protein | ||||||
![]() | TRANSFERASE / demethylase / THF | ||||||
Function / homology | ![]() dimethylsulfoniopropionate demethylase / methyltransferase activity / methylation / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schuller, D.J. / Reisch, C.R. / Moran, M.A. / Whitman, W.B. / Lanzilotta, W.N. | ||||||
![]() | ![]() Title: Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique. Authors: Schuller, D.J. / Reisch, C.R. / Moran, M.A. / Whitman, W.B. / Lanzilotta, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 341.7 KB | Display | ![]() |
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PDB format | ![]() | 279.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.8 KB | Display | ![]() |
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Full document | ![]() | 480.8 KB | Display | |
Data in XML | ![]() | 37.7 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tfhC ![]() 3tfjC ![]() 1v5vS ![]() 1wooS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41886.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Gene synthesized with E. coli codon preferences. Plasmid based on pCYB1. Source: (gene. exp.) ![]() Strain: HTCC1062 / Gene: dmdA, SAR11_0246 / Plasmid: pABX101 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 298 K / pH: 6.8 Details: 25 mM HEPES, 325 mM NaCl, 20% PEG. PEG increased to 30% for cryo. Soaked with DMSP, pH 6.8, Microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2008 / Details: vertical focusing mirrors |
Radiation | Monochromator: double crystal Si(111) cooled with lN2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 99295 / Num. obs: 96714 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.08 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 10 / Num. unique all: 9909 / Rsym value: 0.151 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 1WOO, 1V5V Resolution: 1.6→29.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.843 / SU ML: 0.047 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.111 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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