+Open data
-Basic information
Entry | Database: PDB / ID: 5zq8 | ||||||
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Title | Crystal structure of spRlmCD with U747 stemloop RNA | ||||||
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: 2.18 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 | 5zq8.cif.gz | 206.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zq8.ent.gz | 158.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/5zq8 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/5zq8 | HTTPS FTP |
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-Related structure data
Related structure data | 5zq0C 5zq1C 5zthC 5xj1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 1 - 454 / Label seq-ID: 1 - 454
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-Components
#1: Protein | Mass: 51386.047 Da / Num. of mol.: 2 / 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 #2: RNA chain | Mass: 3875.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae TIGR4 (bacteria) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Ammonium acetate, 0.1M sodium acetate, pH5.2, 20%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9774 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→56.37 Å / Num. obs: 48209 / % possible obs: 87.8 % / Redundancy: 3.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.078 / Rrim(I) all: 0.152 / Net I/σ(I): 6.2 / Num. measured all: 176570 | ||||||||||||||||||||||||||||||
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: 2.18→56.37 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 12.562 / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.4 / ESU R Free: 0.286 / 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: 123.26 Å2 / Biso mean: 39.567 Å2 / Biso min: 17.62 Å2
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Refinement step | Cycle: final / Resolution: 2.18→56.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13362 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.176→2.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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