+Open data
-Basic information
Entry | Database: PDB / ID: 3tma | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of TrmN from Thermus thermophilus | ||||||
Components | methyltransferase | ||||||
Keywords | TRANSFERASE / Rossmann fold methyltransferase / THUMP domain / tRNA methyltransferase | ||||||
Function / homology | Function and homology information tRNA (guanine6-N2)-methyltransferase / tRNA processing / methyltransferase activity / methylation / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Fislage, M. / Roovers, M. / Tuszynska, I. / Bujnicki, J.M. / Droogmans, L. / Versees, W. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life. Authors: Fislage, M. / Roovers, M. / Tuszynska, I. / Bujnicki, J.M. / Droogmans, L. / Versees, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tma.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tma.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tma_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tma_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 3tma_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3tma_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/3tma ftp://data.pdbj.org/pub/pdb/validation_reports/tm/3tma | HTTPS FTP |
-Related structure data
Related structure data | 3tljSC 3tm4C 3tm5C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 39078.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TTC1157, TT_C1157 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q72IH5, Transferases; Transferring one-carbon groups; Methyltransferases |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.89 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 100 mM citrate/phosphate, 15% PEG 6000, 200 mM NaCl, 100 mM sodium citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 27, 2010 |
Radiation | Monochromator: monochromator (horizontally side diffracting Silicon 111 crystal) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 23538 / Num. obs: 23534 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 7.37 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TLJ Resolution: 2.05→44.77 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.886 / SU ML: 0.098 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.157 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.969 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→44.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|