[English] 日本語
Yorodumi- PDB-6tuu: Leishmania infantum Rad51 surrogate LiRadA10 in complex with 5,6,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tuu | ||||||
---|---|---|---|---|---|---|---|
Title | Leishmania infantum Rad51 surrogate LiRadA10 in complex with 5,6,7,8-tetrahydro-2-naphthoic acid | ||||||
Components | DNA repair and recombination protein RadA | ||||||
Keywords | RECOMBINATION / Recombinase / FBDD / Fragment / Surrogate / RadA / Rad51 / Archaeal | ||||||
Function / homology | Function and homology information DNA recombinase assembly / mitotic recombination / DNA strand invasion / DNA strand exchange activity / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Pantelejevs, T. / Hyvonen, M. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: Development of dedicated crystallographic systems for structure-guided drug discovery Authors: Brear, P. / Pantelejevs, T. / Hyvonen, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tuu.cif.gz | 198.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tuu.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 6tuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tuu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6tuu_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6tuu_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 6tuu_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/6tuu ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tuu | HTTPS FTP |
-Related structure data
Related structure data | 5jfgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26592.275 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Gene: radA, PF1926 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036 #2: Chemical | #3: Chemical | ChemComp-NY5 / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.03 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 20 %w/v PEG 1K (Precipitant), 0.1 M Na K Phos 6.2 pH (Buffer), 0.2 M NaCl (Salt) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 1.735→48.5 Å / Num. obs: 80648 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 28.88 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.735→1.765 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 259450 / Rsym value: 0.866 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5jfg Resolution: 1.74→41.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.122
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.76 Å2 / Biso mean: 33.51 Å2 / Biso min: 13.59 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→41.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.74→1.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
|