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Yorodumi- PDB-2nxe: T. thermophilus ribosomal protein L11 methyltransferase (PrmA) in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nxe | ||||||
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Title | T. thermophilus ribosomal protein L11 methyltransferase (PrmA) in complex with S-Adenosyl-L-Methionine | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 2nxe.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nxe.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 2nxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/2nxe ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nxe | HTTPS FTP |
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-Related structure data
Related structure data | 2nxcSC 2nxjC 2nxnC 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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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: Chemical | #3: 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: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: 190 mM Calcium chloride dihydrate, 95mM HEPES-Na, pH 7.5, 26.6% v/v PEG400, 5% glycerol, microbatch under oil, temperature 277K |
-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: 1.75→30 Å / Num. all: 59737 / Num. obs: 59391 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.13 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5929 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2NXC Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.645 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.109 / 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: 31.865 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.794 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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