+Open data
-Basic information
Entry | Database: PDB / ID: 5zth | ||||||
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Title | Crystal structure of spRlmCD with U1939loop RNA at 3.24 angstrom | ||||||
Components |
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Keywords | TRANSFERASE/RNA / methyltransferase / ribosome RNA / S.pneumoniae / intermediate / TRANSFERASE / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information : / RNA modification / RNA methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae serotype 4 (bacteria) Streptococcus pneumoniae TIGR4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å | ||||||
Authors | Jiang, Y.Y. / Yu, H.L. | ||||||
Citation | Journal: PLoS Pathog. / Year: 2018 Title: Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD Authors: Jiang, Y. / Yu, H. / Li, F. / Cheng, L. / Zhu, L. / Shi, Y. / Gong, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zth.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zth.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/5zth ftp://data.pdbj.org/pub/pdb/validation_reports/zt/5zth | HTTPS FTP |
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-Related structure data
Related structure data | 5zq0C 5zq1C 5zq8C 5xj1S 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
#1: Protein | Mass: 51303.023 Da / Num. of mol.: 1 / Mutation: E443Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria) Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1029 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q97R12, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: RNA chain | Mass: 2471.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae TIGR4 (bacteria) |
#3: Chemical | ChemComp-SAH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium dihydrogen Phosphate 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.24→50 Å / Num. obs: 8963 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.314 / Rpim(I) all: 0.106 / Rrim(I) all: 0.332 / Χ2: 0.488 / Net I/σ(I): 1.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XJ1 Resolution: 3.24→50 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.859 / SU B: 25.629 / SU ML: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.59 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 106.77 Å2 / Biso mean: 45.903 Å2 / Biso min: 34.01 Å2
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Refinement step | Cycle: final / Resolution: 3.24→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.24→3.305 Å / Rfactor Rfree error: 0
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