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Yorodumi- PDB-4atn: Crystal structure of C2498 2'-O-ribose methyltransferase RlmM fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4atn | ||||||
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Title | Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli | ||||||
Components | RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 23S rRNA (cytidine2498-2'-O)-methyltransferase / rRNA (cytosine-2'-O-)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Punekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4atn.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4atn.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 4atn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/4atn ftp://data.pdbj.org/pub/pdb/validation_reports/at/4atn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PEXP5-CT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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