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- PDB-5j4h: Structure of humanised RadA-mutant humRadA22F in complex with ind... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j4h | |||||||||
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Title | Structure of humanised RadA-mutant humRadA22F in complex with indole-6-carboxylic acid | |||||||||
![]() | DNA repair and recombination protein RadA | |||||||||
![]() | HYDROLASE / DNA repair / fragment based drug design / humanisation | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.7 KB | Display | ![]() |
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PDB format | ![]() | 124 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.4 KB | Display | ![]() |
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Full document | ![]() | 443.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fosC ![]() 5j4kC ![]() 5j4lC ![]() 5jecC ![]() 5jedC ![]() 5jeeC ![]() 5kddC ![]() 5l8vC ![]() 5lb2C ![]() 5lb4C ![]() 5lbiC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 281 molecules ![](data/chem/img/1F1.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-1F1 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-DMS / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % / Description: elongated plates |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.08M NaCacodylate pH=6.5, 0.16M CaAcetate, 18% PEG 8000, 20% glycerol soaking: 10% DMSO, 5mM compound |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.374→61.122 Å / Num. obs: 44591 / % possible obs: 96.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rsym value: 0.062 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.374→1.378 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2 / % possible all: 76.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: apo_structure Resolution: 1.374→50.157 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 14.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.374→50.157 Å
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Refine LS restraints |
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LS refinement shell |
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