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Yorodumi- PDB-1yjm: Crystal structure of the FHA domain of mouse polynucleotide kinas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yjm | ||||||
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Title | Crystal structure of the FHA domain of mouse polynucleotide kinase in complex with an XRCC4-derived phosphopeptide. | ||||||
Components |
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Keywords | Transferase/DNA BINDING PROTEIN / polynucleotide kinase / FHA domain / XRCC4 phosphopeptide / Transferase-DNA BINDING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping ...polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping / ubiquitin-like ligase-substrate adaptor activity / positive regulation of telomere maintenance via telomerase / double-strand break repair via nonhomologous end joining / site of double-strand break / double-stranded DNA binding / response to oxidative stress / phosphorylation / DNA repair / DNA damage response / nucleolus / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. ...Bernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. / Durocher, D. / Weinfeld, M. / Glover, J.N.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase. Authors: Bernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. / Durocher, D. / Weinfeld, M. / Glover, J.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yjm.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yjm.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yjm ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yjm | HTTPS FTP |
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-Related structure data
Related structure data | 1yj5SC 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is a monomer of full-length polynucleotide kinase. |
-Components
#1: Protein | Mass: 11799.494 Da / Num. of mol.: 3 / Fragment: FHA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pnk / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold 99 References: UniProt: Q9JLV6, polynucleotide 5'-hydroxyl-kinase #2: Protein/peptide | Mass: 1567.457 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: chemically synthesized phospho-peptide #3: Water | ChemComp-HOH / | |
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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: 3.06 Å3/Da / Density % sol: 59.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Na citrate (pH 5.5), 25% PEG 4000, 0.2M Li2SO4, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2004 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 21246 / Num. obs: 18994 / % possible obs: 89.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rsym value: 0.051 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.194 / % possible all: 70.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The FHA domain from the full-length mouse PNK structure, 1YJ5 Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.338 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.637 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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