[English] 日本語
Yorodumi- PDB-8pu1: Structure of the toxin/antitoxin complex FaRel/ATfaRel2 with APCPP -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pu1 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the toxin/antitoxin complex FaRel/ATfaRel2 with APCPP | ||||||
Components |
| ||||||
Keywords | ANTITOXIN / Toxin / toxSAS / RSH / small alormone synthetase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Coprobacillus sp. D7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å | ||||||
Authors | Garcia-Pino, A. / Talavera Perez, A. / Dominguez Molina, L. | ||||||
Funding support | Belgium, 1items
| ||||||
Citation | Journal: To Be Published Title: Structure of the toxin/antitoxin complex FaRel/ATfaRel2 with APCPP Authors: Garcia-Pino, A. / Talavera Perez, A. / Dominguez Molina, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8pu1.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8pu1.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 8pu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/8pu1 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/8pu1 | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 8501.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coprobacillus sp. D7 (bacteria) / Gene: DXB93_19740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E3DY87 |
---|---|
#2: Protein | Mass: 24875.225 Da / Num. of mol.: 1 / Mutation: Y128F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coprobacillus sp. D7 (bacteria) / Gene: DXB93_19735 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E3DY42 |
-Non-polymers , 6 types, 351 molecules
#3: Chemical | ChemComp-POL / #4: Chemical | ChemComp-CAC / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-APC / | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3% v/v 2-Propanol and 0.1 M Sodium, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→52.26 Å / Num. obs: 55679 / % possible obs: 99.95 % / Redundancy: 68.4 % / Biso Wilson estimate: 40.61 Å2 / CC1/2: 1 / Net I/σ(I): 24.47 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 78533 / CC1/2: 0.399 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.702→52.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.091
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.36 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.702→52.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.702→1.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -51.2751 Å / Origin y: -12.968 Å / Origin z: -42.2611 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { *|* } |