+
Open data
-
Basic information
Entry | Database: PDB / ID: 3tfh | ||||||
---|---|---|---|---|---|---|---|
Title | DMSP-dependent demethylase from P. ubique - apo | ||||||
![]() | 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 173.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 137.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457 KB | Display | |
Data in XML | ![]() | 34.9 KB | Display | |
Data in CIF | ![]() | 52.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tfiC ![]() 3tfjC ![]() 1v5vS ![]() 1wooS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.11 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 6.8 Details: 25 mM HEPES, 325 mM NaCl, 20% PEG. PEG increased to 30% for cryo, pH 6.8, Microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 43819 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 34.2 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 13 / Num. unique all: 4385 / Rsym value: 0.201 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entries 1WOO, 1V5V Resolution: 2.1→43.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.226 / SU ML: 0.144 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 34.23 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→43.51 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
|