+Open data
-Basic information
Entry | Database: PDB / ID: 5zq1 | ||||||
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Title | Crystal structure of spRlmCD with U1939loop RNA at 3.10 angstrom | ||||||
Components |
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Keywords | TRANSFERASE/RNA / methyltransferase / Ribosome / 23S RNA / Streptococcus pneumoniae / 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: 3.1 Å | ||||||
Authors | Yu, H.L. / Jiang, Y.Y. | ||||||
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 | 5zq1.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zq1.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/5zq1 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/5zq1 | HTTPS FTP |
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-Related structure data
Related structure data | 5zq0C 5zq8C 5zthC 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: 51171.832 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: 2.42 Å3/Da / Density % sol: 49.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES, pH 5.5, 0.15 M ammonium sulfate, 25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 25, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→40 Å / Num. obs: 10101 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.059 / Rrim(I) all: 0.173 / Χ2: 0.912 / Net I/σ(I): 6.3 / Num. measured all: 84586 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XJ1 Resolution: 3.1→40 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.692 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.55 Å2 / Biso mean: 64.795 Å2 / Biso min: 41.91 Å2
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Refinement step | Cycle: final / Resolution: 3.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.181 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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