+Open data
-Basic information
Entry | Database: PDB / ID: 5fos | ||||||
---|---|---|---|---|---|---|---|
Title | HUMANISED MONOMERIC RADA IN COMPLEX WITH OLIGOMERISATION PEPTIDE | ||||||
Components | (DNA REPAIR AND RECOMBINATION PROTEIN RADA) x 2 | ||||||
Keywords | HYDROLASE / FXXA MOTIF / RECOMBINASE | ||||||
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: 1.35 Å | ||||||
Authors | Sharpe, T. / Moschetti, T. / Fischer, G. / Marsh, M. / Blundell, T.L. / Abell, C. / Hyvonen, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51. Authors: Moschetti, T. / Sharpe, T. / Fischer, G. / Marsh, M.E. / Ng, H.K. / Morgan, M. / Scott, D.E. / Blundell, T.L. / R Venkitaraman, A. / Skidmore, J. / Abell, C. / Hyvonen, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fos.cif.gz | 158.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fos.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fos_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fos_full_validation.pdf.gz | 456.8 KB | Display | |
Data in XML | 5fos_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 5fos_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/5fos ftp://data.pdbj.org/pub/pdb/validation_reports/fo/5fos | HTTPS FTP |
-Related structure data
Related structure data | 5j4hC 5j4kC 5j4lC 5jecC 5jedC 5jeeC 5kddC 5l8vC 5lb2C 5lb4C 5lbiC 1pznS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25502.150 Da / Num. of mol.: 1 / Fragment: ATPASE, UNP RESIDUES 108-349 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PUBS520 References: UniProt: O74036, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 1915.245 Da / Num. of mol.: 1 / Fragment: OLIGOMERISATION PEPTIDE, UNP RESIDUES 93-108 / Source method: obtained synthetically / Source: (synth.) PYROCOCCUS FURIOSUS (archaea) References: UniProt: O74036, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement | ||||
#3: Chemical | ChemComp-PO4 / | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | MUTATIONS I169M, Y201A, V202Y, K221M AND REPLACEMENT OF LOOP 287-300 BY AN N. MUTATIONS I169M, ...MUTATIONS I169M, Y201A, V202Y, K221M AND REPLACEMEN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.2 % / Description: NONE |
---|---|
Crystal grow | pH: 6.2 / Details: 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→36.95 Å / Num. obs: 47394 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.33 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 4.77 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.65 / % possible all: 98.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PZN Resolution: 1.35→36.949 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 15.99 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→36.949 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|