+Open data
-Basic information
Entry | Database: PDB / ID: 5l8v | ||||||
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Title | Apo-structure of humanised RadA-mutant humRadA4 | ||||||
Components | DNA repair and recombination protein RadA | ||||||
Keywords | HYDROLASE / DNA repair / fragment based drug design / humanisation | ||||||
Function / homology | Function and homology information ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Marsh, M. / Fischer, G. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. ...Marsh, M. / Fischer, G. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l8v.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l8v.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 5l8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/5l8v ftp://data.pdbj.org/pub/pdb/validation_reports/l8/5l8v | HTTPS FTP |
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-Related structure data
Related structure data | 5fosC 5j4hC 5j4kC 5j4lC 5jecC 5jedC 5jeeC 5jfgC 5kddC 5lb2C 5lb4C 5lbiC 4a6pS S: Starting model for refinement 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: 24873.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O74036 |
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#2: Chemical | ChemComp-PO4 / |
#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: 2.03 Å3/Da / Density % sol: 39.29 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 12% PEG20K, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å |
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: 1.5→50 Å / Num. obs: 32967 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 17.18 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.063 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 7 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3.25 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A6P Resolution: 1.5→37.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.9448 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.071
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Displacement parameters | Biso mean: 20.3 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→37.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Total num. of bins used: 17
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