+Open data
-Basic information
Entry | Database: PDB / ID: 5lb4 | |||||||||
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Title | Apo-structure of humanised RadA-mutant humRadA14 | |||||||||
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: 1.98 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. | |||||||||
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 | 5lb4.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lb4.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 5lb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/5lb4 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/5lb4 | HTTPS FTP |
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-Related structure data
Related structure data | 5fosC 5j4hC 5j4kC 5j4lC 5jecC 5jedC 5jeeC 5kddC 5l8vC 5lb2C 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: 25508.113 Da / Num. of mol.: 1 Mutation: V168A, I169M, W170Y, Y201A, V202Y, L213Q, V215L, Q216Y, E219S, D220A, K221M, I222M, K223V, L225S, V232Y, H264F, D267M, L274E, Y275F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (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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#2: 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: 39.41 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 25% PEG4000, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97903 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→45 Å / Num. obs: 14305 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.69 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.045 / Net I/σ(I): 20.51 |
Reflection shell | Resolution: 1.98→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.29 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A6P Resolution: 1.98→33.71 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.89 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.179
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Displacement parameters | Biso mean: 38.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→33.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.14 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
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