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Yorodumi- PDB-3tm5: Crystal structure of Trm14 from Pyrococcus furiosus in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tm5 | ||||||
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Title | Crystal structure of Trm14 from Pyrococcus furiosus in complex with sinefungin | ||||||
Components | Crystal structure of Trm14 | ||||||
Keywords | TRANSFERASE / Rossmann fold / methyltransferase / THUMP domain / tRNA methyltransferase | ||||||
Function / homology | Function and homology information tRNA (guanine(6)-N2)-methyltransferase activity / tRNA (guanine6-N2)-methyltransferase / tRNA methylation / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tm5.cif.gz | 161.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tm5.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 3tm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tm5_validation.pdf.gz | 928.5 KB | Display | wwPDB validaton report |
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Full document | 3tm5_full_validation.pdf.gz | 952 KB | Display | |
Data in XML | 3tm5_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 3tm5_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/3tm5 ftp://data.pdbj.org/pub/pdb/validation_reports/tm/3tm5 | HTTPS FTP |
-Related structure data
Related structure data | 3tljSC 3tm4C 3tmaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The asymmetric unit contains two identical molecules connected by NCS |
-Components
#1: Protein | Mass: 42131.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1002 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) References: UniProt: Q8U248, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: 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: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris-acetate, 32% PEG 4000, 15% glycerol, crystal was soaked in crystallization solution containing 1 mM sinefungin, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98 Å | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2011 | |||||||||||||||
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.27→50 Å / Num. all: 80676 / Num. obs: 55944 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 8.6 | |||||||||||||||
Reflection shell | Resolution: 2.27→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.08 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3TLJ Resolution: 2.27→48.02 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.909 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.046 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.383 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2756 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→48.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.206→2.263 Å / Total num. of bins used: 20 |