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Yorodumi- PDB-2nxj: T.thermophilus ribosomal protein L11 methyltransferase (PrmA) in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nxj | ||||||
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Title | T.thermophilus ribosomal protein L11 methyltransferase (PrmA) in space group P 21 21 2 | ||||||
Components | Ribosomal protein L11 methyltransferaseRibosome | ||||||
Keywords | TRANSFERASE / S-Adenosyl-L-Methionine dependent methyltransferase / postranslational modification | ||||||
Function / homology | Function and homology information histone methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Demirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G. | ||||||
Citation | Journal: Embo J. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nxj.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nxj.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 2nxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/2nxj ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nxj | HTTPS FTP |
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-Related structure data
Related structure data | 2nxcC 2nxeC 2nxnC 1nxcS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27661.807 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: prmA / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) References: UniProt: Q84BQ9, Transferases; Transferring one-carbon groups; Methyltransferases #2: 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: 2.86 Å3/Da / Density % sol: 57.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.7 M Ammonium sulfate, 85 mM HEPES-Na, pH 7.5, 1.7% w/v PEG400, 15% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9797 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / 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: 2.3→50 Å / Num. all: 29480 / Num. obs: 28554 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2530 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1NXC Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.687 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.254 / 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: 48.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.357 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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