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- PDB-2nxn: T. thermophilus ribosomal protein L11 methyltransferase (PrmA) in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nxn | ||||||
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Title | T. thermophilus ribosomal protein L11 methyltransferase (PrmA) in complex with ribosomal protein L11 | ||||||
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![]() | TRANSFERASE / S-Adenosyl-L-Methionine dependent methyltransferase / post-translational modification | ||||||
Function / homology | ![]() histone methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / large ribosomal subunit rRNA binding / methylation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Demirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G. | ||||||
![]() | ![]() Title: Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA. Authors: Demirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87 KB | Display | ![]() |
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PDB format | ![]() | 66.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.7 KB | Display | ![]() |
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Full document | ![]() | 449.4 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxcSC ![]() 2nxeC ![]() 2nxjC ![]() 1mmsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27661.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q84BQ9, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Protein | Mass: 15526.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25.5 % w/v PEG4000, 120 mM Sodium Acetate, 85mM TRIS, pH 8.5, 15 % v/v glycerol, 4% v/v 1,1,1,3,3,3-Hexafluoro-2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 18545 / Num. obs: 18330 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1766 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entries 1MMS, 2NXC Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.522 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.281 / 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: 62.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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