+Open data
-Basic information
Entry | Database: PDB / ID: 5j4l | |||||||||
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Title | Apo-structure of humanised RadA-mutant humRadA22F | |||||||||
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: 1.13 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. | |||||||||
Funding support | United Kingdom, 2items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j4l.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j4l.ent.gz | 130.8 KB | Display | PDB format |
PDBx/mmJSON format | 5j4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j4l_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 5j4l_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 5j4l_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 5j4l_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j4l ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4l | HTTPS FTP |
-Related structure data
Related structure data | 5fosC 5j4hC 5j4kC 5jecC 5jedC 5jeeC 5kddC 5l8vC 5lb2C 5lb4C 5lbiC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.49 % / 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% PEG8000, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→30 Å / Num. obs: 148188 / % possible obs: 93.7 % / Redundancy: 3.06 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.999 / Rsym value: 0.051 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.13→1.2 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.03 / % possible all: 67.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→26.764 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→26.764 Å
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Refine LS restraints |
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LS refinement shell |
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