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Yorodumi- PDB-3lhd: Crystal structure of P. abyssi tRNA m1A58 methyltransferase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lhd | ||||||
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Title | Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine | ||||||
Components | SAM-dependent methyltransferase, putative | ||||||
Keywords | TRANSFERASE / RNA methyltransferase / m1A / TrmI / intermolecular contacts / region-specificity / tetramer / disulfide bond / hyperthermostability / Methyltransferase | ||||||
Function / homology | Function and homology information tRNA (adenine57-N1/adenine58-N1)-methyltransferase / tRNA (adenine(57)-N1)/(adenine(58)-N1)-methyltransferase activity / tRNA (adenine(58)-N1)-methyltransferase activity / tRNA (m1A) methyltransferase complex / tRNA methylation Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Guelorget, A. / Golinelli-Pimpaneau, B. / Wouters, J. / Barbey, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2010 Title: Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Authors: Guelorget, A. / Roovers, M. / Guerineau, V. / Barbey, C. / Li, X. / Golinelli-Pimpaneau, B. #1: Journal: Nucleic Acids Res. / Year: 2004 Title: A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase Authors: Roovers, M. / Wouters, J. / Bujnicki, J.M. / Tricot, C. / Stalon, V. / Grosjean, H. / Droogmans, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lhd.cif.gz | 209.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lhd.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lhd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3lhd_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3lhd_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 3lhd_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/3lhd ftp://data.pdbj.org/pub/pdb/validation_reports/lh/3lhd | HTTPS FTP |
-Related structure data
Related structure data | 3lgaC 3mb5C 1i9gS 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: 28920.662 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Gene: PAB0283 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q9V1J7, EC: 2.1.1.36 #2: Chemical | ChemComp-SAH / #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: 2.76 Å3/Da / Density % sol: 55.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M ammonium sulfate, 0.1M sodium acetate, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→65.1 Å / Num. all: 38766 / Num. obs: 38327 / % possible obs: 94.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.59→2.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 2.4 / % possible all: 68.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I9G Resolution: 2.59→58.78 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / SU B: 12.242 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.932 / ESU R Free: 0.365 / 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: 51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→58.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.592→2.659 Å / Total num. of bins used: 20
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