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Yorodumi- PDB-3dcm: Crystal structure of the Thermotoga maritima SPOUT family RNA-met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dcm | ||||||
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Title | Crystal structure of the Thermotoga maritima SPOUT family RNA-methyltransferase protein Tm1570 in complex with S-adenosyl-L-methionine | ||||||
Components | Uncharacterized protein TM_1570 | ||||||
Keywords | TRANSFERASE / Trefoil knot / SPOUT Mtase / AdoMet binding | ||||||
Function / homology | Function and homology information tRNA (guanine-N(1)-)-methyltransferase, C-terminal / SAM-dependent RNA methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Kim, D.J. / Kim, H.S. / Lee, S.J. / Suh, S.W. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure of Thermotoga maritima SPOUT superfamily RNA methyltransferase Tm1570 in complex with S-adenosyl-L-methionine Authors: Kim, D.J. / Kim, H.S. / Lee, S.J. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dcm.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dcm.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 3dcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dcm_validation.pdf.gz | 739.3 KB | Display | wwPDB validaton report |
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Full document | 3dcm_full_validation.pdf.gz | 742.1 KB | Display | |
Data in XML | 3dcm_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3dcm_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/3dcm ftp://data.pdbj.org/pub/pdb/validation_reports/dc/3dcm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22008.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1570 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9X1Q6 |
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#2: Chemical | ChemComp-SAM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.37 % / Mosaicity: 0.906 ° |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Tris-HCl pH 7.0, 200mM calcium acetate, 20% (v/v) PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. obs: 14038 / % possible obs: 98.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.071 / Χ2: 2.005 / Net I/σ(I): 14.5 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.247 / Num. unique all: 1282 / Χ2: 1.432 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→17.43 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.885 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.379 Å2
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Refinement step | Cycle: LAST / Resolution: 2→17.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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