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Yorodumi- PDB-4cng: Crystal structure of Sulfolobus acidocaldarius TrmJ in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cng | ||||||
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Title | Crystal structure of Sulfolobus acidocaldarius TrmJ in complex with S-adenosyl-L-Homocysteine | ||||||
Components | SPOU RRNA METHYLASE | ||||||
Keywords | TRANSFERASE / TRNA 2'-O-METHYLTRANSFERASE / SPOUT | ||||||
Function / homology | Function and homology information RNA methyltransferase activity / RNA methylation / tRNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | SULFOLOBUS ACIDOCALDARIUS (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Van Laer, B. / Somme, J. / Roovers, M. / Steyaert, J. / Droogmans, L. / Versees, W. | ||||||
Citation | Journal: RNA / Year: 2014 Title: Characterization of Two Homologous 2'-O-Methyltransferases Showing Different Specificities for Their tRNA Substrates. Authors: Somme, J. / Van Laer, B. / Roovers, M. / Steyaert, J. / Versees, W. / Droogmans, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cng.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cng.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 4cng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cng ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cng | HTTPS FTP |
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-Related structure data
Related structure data | 4cndC 4cneC 4cnfSC 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: 29080.924 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: TRNA CM32 METHYLTRANSFERASE Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic) Strain: ATCC33909 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: Q4JB16, tRNA (cytidine32/uridine32-2'-O)-methyltransferase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.27 Å3/Da / Density % sol: 45.85 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 0.2M KBR, 0.1 M NA-ACETATE PH 5.5, 20% PEG2000MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→43 Å / Num. obs: 128921 / % possible obs: 97.5 % / Observed criterion σ(I): 1.2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.2 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CNF Resolution: 1.1→43.26 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.344 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→43.26 Å
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Refine LS restraints |
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