+Open data
-Basic information
Entry | Database: PDB / ID: 5fpk | ||||||
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Title | MONOMERIC RADA IN COMPLEX WITH FATA TETRAPEPTIDE | ||||||
Components |
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Keywords | HYDROLASE / RADA / FXXA MOTIF / RECOMBINASE | ||||||
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) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.343 Å | ||||||
Authors | Scott, D.E. / Marsh, M. / Blundell, T.L. / Abell, C. / Hyvonen, M. | ||||||
Citation | Journal: FEBS Lett. / Year: 2016 Title: Structure Activity Relationship of the Peptide Binding Motif Mediating the Rad51:Brca2 Protein-Protein Interaction. Authors: Scott, D.E. / Marsh, M. / Blundell, T.L. / 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 | 5fpk.cif.gz | 163.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fpk.ent.gz | 131.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpk ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpk | HTTPS FTP |
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-Related structure data
Related structure data | 5fotC 5fouC 5fovC 5fowC 5foxC 4b3bS C: citing same article (ref.) S: Starting model for refinement |
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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: 25510.150 Da / Num. of mol.: 1 / Fragment: ATPASE, UNP RESIDUES 108-349 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PUBS520 / References: UniProt: O74036 |
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#2: Protein/peptide | Mass: 432.494 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: ACETYLATED AT THE N-TERMINUS AND AMIDATED IN THE C-TERMINUS Source: (synth.) HOMO SAPIENS (human) |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | MUTATION R288N AND DELETION OF LOOP 289-300. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE |
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Crystal grow | pH: 6.2 / Details: 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→49.8 Å / Num. obs: 47749 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 6.98 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.41 |
Reflection shell | Resolution: 1.34→1.42 Å / Redundancy: 6.24 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.98 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4B3B Resolution: 1.343→43.723 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 14.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.343→43.723 Å
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Refine LS restraints |
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LS refinement shell |
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