+Open data
-Basic information
Entry | Database: PDB / ID: 4cnf | ||||||
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Title | Crystal structure of Sulfolobus acidocaldarius TrmJ | ||||||
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: 1.4 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 | 4cnf.cif.gz | 147.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cnf.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cnf ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cnf | HTTPS FTP |
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-Related structure data
Related structure data | 4cndSC 4cneC 4cngC 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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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 Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic) 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-PEG / | #4: Chemical | ChemComp-MTA / | #5: 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: 2.22 Å3/Da / Density % sol: 44.51 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 0.2 M KBR, 0.1M 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: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Mar 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→43 Å / Num. obs: 63289 / % possible obs: 99.9 % / Observed criterion σ(I): 1.2 / Redundancy: 14.4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 14 % / Mean I/σ(I) obs: 1.2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CND Resolution: 1.4→42.69 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.058 / 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: 21.534 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→42.69 Å
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Refine LS restraints |
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