+Open data
-Basic information
Entry | Database: PDB / ID: 3tfi | ||||||
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Title | DMSP-dependent demethylase from P. ubique - with substrate DMSP | ||||||
Components | GcvT-like Aminomethyltransferase protein | ||||||
Keywords | TRANSFERASE / demethylase / THF | ||||||
Function / homology | Function and homology information dimethylsulfoniopropionate demethylase / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Candidatus Pelagibacter ubique (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Schuller, D.J. / Reisch, C.R. / Moran, M.A. / Whitman, W.B. / Lanzilotta, W.N. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tfi.cif.gz | 341.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tfi.ent.gz | 279.3 KB | Display | PDB format |
PDBx/mmJSON format | 3tfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/3tfi ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tfi | HTTPS FTP |
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-Related structure data
Related structure data | 3tfhC 3tfjC 1v5vS 1wooS C: citing same article (ref.) 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: 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.) Candidatus Pelagibacter ubique (bacteria) Strain: HTCC1062 / Gene: dmdA, SAR11_0246 / Plasmid: pABX101 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10F' / References: UniProt: Q4FP21, aminomethyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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