+Open data
-Basic information
Entry | Database: PDB / ID: 6abo | ||||||
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Title | human XRCC4 and IFFO1 complex | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / complex / coiled-coil | ||||||
Function / homology | Function and homology information FHA domain binding / positive regulation of ligase activity / DNA double-strand break attachment to nuclear envelope / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / intermediate filament ...FHA domain binding / positive regulation of ligase activity / DNA double-strand break attachment to nuclear envelope / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / intermediate filament / nuclear inner membrane / cellular response to lithium ion / 2-LTR circle formation / response to X-ray / SUMOylation of DNA damage response and repair proteins / Nonhomologous End-Joining (NHEJ) / nuclear matrix / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Li, J. / Liu, L. / Liang, H. / Liu, Y. / Xu, D. | ||||||
Citation | Journal: Nat.Cell Biol. / Year: 2019 Title: The nucleoskeleton protein IFFO1 immobilizes broken DNA and suppresses chromosome translocation during tumorigenesis. Authors: Li, W. / Bai, X. / Li, J. / Zhao, Y. / Liu, J. / Zhao, H. / Liu, L. / Ding, M. / Wang, Q. / Shi, F.Y. / Hou, M. / Ji, J. / Gao, G. / Guo, R. / Sun, Y. / Liu, Y. / Xu, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6abo.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6abo.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 6abo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/6abo ftp://data.pdbj.org/pub/pdb/validation_reports/ab/6abo | HTTPS FTP |
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-Related structure data
Related structure data | 1ik9S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26145.500 Da / Num. of mol.: 1 / Fragment: UNP residues 1-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Plasmid: pRSFDuet / Production host: Escherichia coli (E. coli) / References: UniProt: Q13426 | ||||
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#2: Protein | Mass: 9817.137 Da / Num. of mol.: 1 / Fragment: UNP residues 453-529 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFFO1, IFFO / Plasmid: pRSFDuet / Details (production host): Inserted into the MCSII / Production host: Escherichia coli (E. coli) / References: UniProt: Q0D2I5 | ||||
#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.61 Å3/Da / Density % sol: 78.08 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M Sodium cacodylate pH6.0, 50mM Calcium acetate, 20-25% MPD, 1M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9201 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 24309 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 34.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.047 / Rrim(I) all: 0.158 / Rsym value: 0.151 / Χ2: 0.926 / Net I/σ(I): 14.61 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 1207 / CC1/2: 0.94 / Rpim(I) all: 0.258 / Rrim(I) all: 0.835 / Rsym value: 0.793 / Χ2: 0.805 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IK9 Resolution: 2.65→44.64 Å / SU ML: 0.2799 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6337
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→44.64 Å
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Refine LS restraints |
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LS refinement shell |
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