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Open data
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Basic information
Entry | Database: PDB / ID: 5jec | ||||||
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Title | Apo-structure of humanised RadA-mutant humRadA33F | ||||||
![]() | 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. | ||||||
![]() | ![]() 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 | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 77 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
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Full document | ![]() | 450.2 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fosC ![]() 5j4hC ![]() 5j4kC ![]() 5j4lSC ![]() 5jedC ![]() 5jeeC ![]() 5kddC ![]() 5l8vC ![]() 5lb2C ![]() 5lb4C ![]() 5lbiC S: Starting model for refinement 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25239.799 Da / Num. of mol.: 2 Mutation: S167K, V168A, I169M, W170Y, N175G, I182L, R183L, D192S, P193G D194S, E195D, K198D, H199N, I200V, Y201A, V202Y, E219S, K221M, I222M, K223V, V232Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 22% PEG3350, 0.1M BisTris pH=5.0, 0.2M Li2SO4 / Temp details: Temperature stabilised in incubator |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97631 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→78.594 Å / Num. obs: 21095 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 45.63 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.193 / Rsym value: 0.21 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.34→2.348 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.462 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5J4L Resolution: 2.34→78.59 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9013 / SU R Cruickshank DPI: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.341 / SU Rfree Blow DPI: 0.228 / SU Rfree Cruickshank DPI: 0.23
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Displacement parameters | Biso mean: 39.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.315 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.34→78.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.34→2.45 Å / Total num. of bins used: 11
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