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Yorodumi- PDB-5l0z: Crystal Structure of AdoMet bound rRNA methyltransferase from Sin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l0z | ||||||
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Title | Crystal Structure of AdoMet bound rRNA methyltransferase from Sinorhizobium meliloti | ||||||
Components | Probable RNA methyltransferase, TrmH family | ||||||
Keywords | TRANSFERASE / SPOUT Methyltransferase / AdoMet binding / Trefoil knot | ||||||
Function / homology | Function and homology information RNA methyltransferase activity / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Dey, D. / Hegde, R.P. / Almo, S.C. / Ramakumar, S. / Ramagopal, U.A. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of AdoMet bound rRNA methyltransferase from Sinorhizobium meliloti Authors: Dey, D. / Hegde, R.P. / Almo, S.C. / Ramakumar, S. / Ramagopal, U.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l0z.cif.gz | 207.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l0z.ent.gz | 174.1 KB | Display | PDB format |
PDBx/mmJSON format | 5l0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l0z_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5l0z_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5l0z_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 5l0z_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/5l0z ftp://data.pdbj.org/pub/pdb/validation_reports/l0/5l0z | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31565.287 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria) Strain: 1021 / Gene: SMc01130 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL References: UniProt: Q92SJ4, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-CO / #3: Chemical | #4: Chemical | |
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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: 2.32 Å3/Da / Density % sol: 46.98 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5mM Cobalt chloride , 5mM Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 9% wt/vol polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→65.94 Å / Num. obs: 13571 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.86 / Net I/σ(I): 28.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→65.94 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.862 / SU B: 39.924 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 Details: 1.542, 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.424 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→65.94 Å
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Refine LS restraints |
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