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- PDB-3egv: Ribosomal protein L11 methyltransferase (PrmA) in complex with tr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3egv | ||||||||||||
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Title | Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11 | ||||||||||||
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![]() | TRANSFERASE/RIBOSOMAL PROTEIN / post-translational modification / multiple methyltransferase / Methyltransferase / Transferase / Methylation / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / TRANSFERASE-RIBOSOMAL PROTEIN COMPLEX | ||||||||||||
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: Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase. 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 | ![]() | 92.9 KB | Display | ![]() |
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PDB format | ![]() | 67.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.7 KB | Display | ![]() |
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Full document | ![]() | 793.1 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cjqC ![]() 3cjrC ![]() 3cjsC ![]() 3cjtC ![]() 2nxcS ![]() 2nxnS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 27661.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: cytoplasm / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q84BQ9, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Protein | Mass: 15511.098 Da / Num. of mol.: 1 / Mutation: K16A Source method: isolated from a genetically manipulated source Details: cytoplasm / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 422 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SAH / | ||||||
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#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-IOD / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.64 % |
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Crystal grow | Temperature: 277 K / Method: microbatch technique under oil / pH: 6.5 Details: 160 mM calcium acetate hydrate, 80 mM sodium cacodylate, 14.4% w/v PEG8000, 20% v/v glycerol, 4mM AdoMet, pH 6.5, microbatch technique under oil, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2006 Details: Variable vertical and fixed horizontal slits. KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit ...Details: Variable vertical and fixed horizontal slits. KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source and ~6 m from sample position. Mirror system consisting of two vertically stacked, fused silica, spherical mirrors, to provide vertical focusing and harmonic rejection. One of the mirrors is rhodium coated and the other is uncoated. Located ~19.7 m from source. |
Radiation | Monochromator: KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source ...Monochromator: KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source and ~6 m from sample position. 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. obs: 48051 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2 / Num. unique all: 9414 / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entries 2NXC, 2NXN Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.55 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / 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: 33.628 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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