[English] 日本語
Yorodumi- PDB-5j4k: Structure of humanised RadA-mutant humRadA22F in complex with 1-I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j4k | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of humanised RadA-mutant humRadA22F in complex with 1-Indane-6-carboxylic acid | ||||||
Components | DNA repair and recombination protein RadA | ||||||
Keywords | HYDROLASE / DNA repair / fragment based drug design / humanisation | ||||||
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: 1.346 Å | ||||||
Authors | Fischer, G. / Marsh, M. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. ...Fischer, G. / Marsh, M. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. / Blundell, T.L. / 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 | 5j4k.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5j4k.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 5j4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j4k_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5j4k_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 5j4k_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5j4k_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j4k ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4k | HTTPS FTP |
-Related structure data
Related structure data | 5fosC 5j4hC 5j4lC 5jecC 5jedC 5jeeC 5kddC 5l8vC 5lb2C 5lb4C 5lbiC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25398.896 Da / Num. of mol.: 1 Mutation: V168A, I169M, W170Y, I182L, K198D, H199N, I200V, Y201A, V202Y, K221M 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 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036 |
---|
-Non-polymers , 5 types, 246 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-6FZ / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.73 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.08M NaCacodylate pH=6.5, 0.16M CaAcetate, 18% PEG8000, 20%glycerol soaking: 10% DMSO, 5mM compound |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.346→50.204 Å / Num. obs: 46330 / % possible obs: 94.4 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.346→1.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2.1 / % possible all: 58.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo_structure Resolution: 1.346→50.204 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.15
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.346→50.204 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|