+Open data
-Basic information
Entry | Database: PDB / ID: 5jed | ||||||
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Title | Apo-structure of humanised RadA-mutant humRadA28 | ||||||
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: 1.332 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 | 5jed.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jed.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jed_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
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Full document | 5jed_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 5jed_validation.xml.gz | 13 KB | Display | |
Data in CIF | 5jed_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/5jed ftp://data.pdbj.org/pub/pdb/validation_reports/je/5jed | HTTPS FTP |
-Related structure data
Related structure data | 5fosC 5j4hC 5j4kC 5j4lSC 5jecC 5jeeC 5kddC 5l8vC 5lb2C 5lb4C 5lbiC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25628.178 Da / Num. of mol.: 1 Mutation: S167K, V168A, I169M, W170Y, I182L, K198D, H199N, I200V, Y201A, V202Y, L213Q, V215L, Q216Y, E219S, 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) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036 |
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-Non-polymers , 5 types, 205 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-MRD / ( |
#5: Chemical | ChemComp-CL / |
#6: 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 Å3/Da / Density % sol: 38.62 % / Description: rods |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M NaCacodylate pH=6.5, 5% PEG8000, 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.332→37.72 Å / Num. obs: 45801 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Rsym value: 0.103 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.332→1.337 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.086 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5j4l Resolution: 1.332→37.72 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.353 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.216 Å2
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Refinement step | Cycle: 1 / Resolution: 1.332→37.72 Å
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Refine LS restraints |
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