[English] 日本語
Yorodumi- PDB-6l8e: Crystal structure of heterohexameric YoeB-YefM complex bound to 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l8e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of heterohexameric YoeB-YefM complex bound to 26bp-DNA | ||||||
Components |
| ||||||
Keywords | ANTITOXIN/TOXIN/DNA / toxin-antitoxin / microbial RNase / YoeB / Staphylococcus aureus / TOXIN / ANTITOXIN-TOXIN-DNA complex | ||||||
Function / homology | Function and homology information RNA catabolic process / endonuclease activity / negative regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Yue, J. / Xue, L. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system. Authors: Xue, L. / Yue, J. / Ke, J. / Khan, M.H. / Wen, W. / Sun, B. / Zhu, Z. / Niu, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6l8e.cif.gz | 303.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6l8e.ent.gz | 194.4 KB | Display | PDB format |
PDBx/mmJSON format | 6l8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/6l8e ftp://data.pdbj.org/pub/pdb/validation_reports/l8/6l8e | HTTPS FTP |
---|
-Related structure data
Related structure data | 6l8fC 7cuaC 2a6qS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9442.584 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325 / Gene: SAOUHSC_02692 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2G285 #2: Protein | Mass: 10457.985 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325 / Gene: SAOUHSC_02691 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2G286 #3: DNA chain | Mass: 8006.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: DNA chain | Mass: 7962.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 68.99 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→92.48 Å / Num. obs: 89409 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.03 / Rrim(I) all: 0.083 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.35→2.39 Å / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4434 / CC1/2: 0.791 / Rpim(I) all: 0.403 / Rrim(I) all: 1.147 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A6Q Resolution: 2.35→53.51 Å / SU ML: 0.2967 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1748 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→53.51 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|