+Open data
-Basic information
Entry | Database: PDB / ID: 5kdd | ||||||
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Title | Apo-structure of humanised RadA-mutant humRadA22 | ||||||
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: 1.99 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kdd.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kdd.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kdd_validation.pdf.gz | 464.1 KB | Display | wwPDB validaton report |
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Full document | 5kdd_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | 5kdd_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 5kdd_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kdd ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kdd | HTTPS FTP |
-Related structure data
Related structure data | 5fosC 5j4hC 5j4kC 5j4lC 5jecC 5jedC 5jeeC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25542.064 Da / Num. of mol.: 2 Mutation: V168A, I169M, W170Y, I182L, K198D, H199N, I200V, Y201A, V202Y, L213Q, V215L, Q216Y, E219S, D220A, K221M, I222M, K223V, L225S, V232Y, K263R, H264F, A266R, D267M, L274E, Y275F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.988→84.748 Å / Num. obs: 31086 / % possible obs: 95.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 20.83 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.183 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.988→1.994 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.1 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→84.748 Å / Cor.coef. Fo:Fc: 0.8605 / Cor.coef. Fo:Fc free: 0.8384 / SU R Cruickshank DPI: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.219 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.174
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Displacement parameters | Biso mean: 25.13 Å2
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Refinement step | Cycle: 1 / Resolution: 1.99→84.748 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.06 Å / Total num. of bins used: 16
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