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Yorodumi- PDB-4b17: Crystal structure of C2498 2'-O-ribose methyltransferase RlmM fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b17 | ||||||
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Title | Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli in complex with S-adenosylmethionine | ||||||
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 / rRNA processing / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b17.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b17.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 4b17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b17_validation.pdf.gz | 720 KB | Display | wwPDB validaton report |
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Full document | 4b17_full_validation.pdf.gz | 724.5 KB | Display | |
Data in XML | 4b17_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4b17_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/4b17 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/4b17 | HTTPS FTP |
-Related structure data
Related structure data | 4atnSC 4aukC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 105 molecules
#2: Chemical | ChemComp-SAM / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-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: 48.5 % / 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 MAR165 / Detector: CCD / Date: Mar 18, 2012 / Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL |
Radiation | Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→28.87 Å / Num. obs: 12983 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 30.97 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.37 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.27 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ATN Resolution: 2.6→28.874 Å / SU ML: 0.24 / σ(F): 2 / Phase error: 17.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.128 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→28.874 Å
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Refine LS restraints |
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LS refinement shell |
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