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- PDB-4atn: Crystal structure of C2498 2'-O-ribose methyltransferase RlmM fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4atn | ||||||
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Title | Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli | ||||||
![]() | RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() 23S rRNA (cytidine2498-2'-O)-methyltransferase / rRNA (cytosine-2'-O-)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Punekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M. | ||||||
![]() | ![]() Title: Crystal Structure of Rlmm, the 2'O-Ribose Methyltransferase for C2498 of Escherichia Coli 23S Rrna. Authors: Punekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.9 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478 KB | Display | ![]() |
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Full document | ![]() | 484.8 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 43092.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0ADR6, 23S rRNA (cytidine2498-2'-O)-methyltransferase | ||||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | CATALYZES THE 2'-O-METHYLATIO | Sequence details | HAS 6XHIS-TAG AT THE C-TERMINAL END | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.3 M AMMONIUM TARTRATE DIBASIC PH 7.0, 20% PEG 3350, 3.0% DEXTRAN SULFATE SODIUM SALT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Mar 7, 2012 |
Radiation | Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING OPTICS MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→28.77 Å / Num. obs: 30022 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 33.02 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.5 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MODEL OBTAINED FROM K2PTCL4 DERIVATIVE CRYSTAL DATA Resolution: 1.95→28.769 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 19.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.848 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→28.769 Å
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Refine LS restraints |
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LS refinement shell |
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