+Open data
-Basic information
Entry | Database: PDB / ID: 3sr2 | ||||||
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Title | Crystal Structure of Human XLF-XRCC4 Complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/PROTEIN BINDING / XRCC4 / XLF / NHEJ / DNA Repair / DNA / DNA Ligases / DNA-Binding Proteins / Dimerization / Humans / Protein Structure / Quaternary / Complex / Non-Homologous End Joining (NHEJ) / DNA ligase IV / Ku / XLF-XRCC4 / Protein DNA-interaction / DNA BINDING PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / 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 / response to ionizing radiation ...FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / 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 / response to ionizing radiation / cellular response to lithium ion / 2-LTR circle formation / T cell differentiation / response to X-ray / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / B cell differentiation / central nervous system development / Nonhomologous End-Joining (NHEJ) / fibrillar center / 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: 3.9708 Å | ||||||
Authors | Hammel, M. / Classen, S. / Tainer, J.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair. Authors: Hammel, M. / Rey, M. / Yu, Y. / Mani, R.S. / Classen, S. / Liu, M. / Pique, M.E. / Fang, S. / Mahaney, B.L. / Weinfeld, M. / Schriemer, D.C. / Lees-Miller, S.P. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sr2.cif.gz | 252.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sr2.ent.gz | 197.8 KB | Display | PDB format |
PDBx/mmJSON format | 3sr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sr2_validation.pdf.gz | 506 KB | Display | wwPDB validaton report |
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Full document | 3sr2_full_validation.pdf.gz | 631.1 KB | Display | |
Data in XML | 3sr2_validation.xml.gz | 61 KB | Display | |
Data in CIF | 3sr2_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/3sr2 ftp://data.pdbj.org/pub/pdb/validation_reports/sr/3sr2 | HTTPS FTP |
-Related structure data
Related structure data | 2r9aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16256.343 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q13426 #2: Protein | Mass: 25868.922 Da / Num. of mol.: 4 / Fragment: UNP Residues 1-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q9H9Q4 |
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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: 3.96 Å3/Da / Density % sol: 68.93 % |
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Crystal grow | Temperature: 303.15 K / Method: vapor diffusion / pH: 7 Details: protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, ...Details: protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.9→70 Å / Num. all: 26221 / Num. obs: 26221 / % possible obs: 98.8 % / Observed criterion σ(I): 1.7 / Redundancy: 23.8 % / Rmerge(I) obs: 0.131 / Χ2: 1.098 / Net I/σ(I): 2.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R9A Resolution: 3.9708→67.436 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5821 / SU ML: 0.92 / σ(F): 0.24 / Phase error: 43.79 / 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 / Bsol: 40 Å2 / ksol: 0.293 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80 Å2 / Biso mean: 80 Å2 / Biso min: 80 Å2
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Refinement step | Cycle: LAST / Resolution: 3.9708→67.436 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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