+
Open data
-
Basic information
Entry | Database: PDB / ID: 5zq8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of spRlmCD with U747 stemloop RNA | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/RNA / methyltransferase / ribosome / 23S RNA / Streptococcus pneumoniae / TRANSFERASE / TRANSFERASE-RNA complex | ||||||
Function / homology | ![]() rRNA (uridine-C5-)-methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, Y.Y. / Yu, H.L. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 206.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 158.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 972.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 987.7 KB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 48.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zq0C ![]() 5zq1C ![]() 5zthC ![]() 5xj1S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / 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: _ / Auth seq-ID: 1 - 454 / Label seq-ID: 1 - 454
|
-
Components
#1: Protein | Mass: 51386.047 Da / Num. of mol.: 2 / Mutation: E443Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1029 Production host: ![]() ![]() 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.) ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % |
---|---|
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 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→56.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.176→2.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|