[English] 日本語
Yorodumi- PDB-6tuo: Crystal structure of Archaeoglobus fulgidus Argonaute protein wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tuo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / ARGONAUTE / PIWI DOMAIN / PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus (archaea) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Grazulis, S. / Zaremba, M. | ||||||
Citation | Journal: To be published Title: Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT Authors: Golovinas, E. / Manakova, E. / Sasnauskas, G. / Zaremba, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tuo.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tuo.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 6tuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/6tuo ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tuo | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ytuS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein / DNA chain , 2 types, 3 molecules ARS
#1: Protein | Mass: 50921.121 Da / Num. of mol.: 1 / Fragment: Arhaeoglobus fulgidus Argonaute protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea) Strain: DSM 4304 / Gene: AF_1318 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O28951 |
---|---|
#2: DNA chain | Mass: 4278.815 Da / Num. of mol.: 2 / Fragment: oligodeoxyribonucleotide / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Non-polymers , 6 types, 360 molecules
#3: Chemical | ChemComp-MG / | ||||||
---|---|---|---|---|---|---|---|
#4: Chemical | ChemComp-CL / | ||||||
#5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
---|---|
Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Na-Cacodylate pH 5.5 0.05 M, KCl_0.2 M, MgCl2 0.01 M, PEG4000 5% (w/v), glycerol 5% (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2018 / Details: silica substrate + Rh coating | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Oxford-FMB, UK; Si(111) or Si(311); both crystals LN2 cooled, fixed exit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→99.63 Å / Num. all: 349485 / Num. obs: 53664 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Net I/σ(I): 20.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | R rigid body: 0.461
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 1ytu Resolution: 1.8→54.901 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 27.38
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.13 Å2 / Biso mean: 48.285 Å2 / Biso min: 15.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→54.901 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|