+Open data
-Basic information
Entry | Database: PDB / ID: 4wja | ||||||||||||
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Title | Crystal Structure of PAXX | ||||||||||||
Components | Uncharacterized protein C9orf142 | ||||||||||||
Keywords | DNA BINDING PROTEIN / DNA repair / DSB | ||||||||||||
Function / homology | Function and homology information nonhomologous end joining complex / DNA polymerase binding / double-strand break repair via nonhomologous end joining / site of double-strand break / molecular adaptor activity / DNA damage response / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||||||||
Authors | Xing, M. / Yang, M. / Huo, W. / Feng, F. / Wei, L. / Ning, S. / Yan, Z. / Li, W. / Wang, Q. / Hou, M. ...Xing, M. / Yang, M. / Huo, W. / Feng, F. / Wei, L. / Ning, S. / Yan, Z. / Li, W. / Wang, Q. / Hou, M. / Dong, C. / Guo, R. / Gao, G. / Ji, J. / Lan, L. / Liang, H. / Xu, D. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2015 Title: Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway. Authors: Xing, M. / Yang, M. / Huo, W. / Feng, F. / Wei, L. / Jiang, W. / Ning, S. / Yan, Z. / Li, W. / Wang, Q. / Hou, M. / Dong, C. / Guo, R. / Gao, G. / Ji, J. / Zha, S. / Lan, L. / Liang, H. / Xu, D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wja.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wja.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/4wja ftp://data.pdbj.org/pub/pdb/validation_reports/wj/4wja | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17305.395 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C9orf142 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9BUH6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.24M Ammonium sulfate, 0.1M Bis-Tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→79.523 Å / Num. obs: 12287 / % possible obs: 99.3 % / Redundancy: 20 % / Net I/σ(I): 69.64 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 2.6→38.475 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.03 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.475 Å
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Refine LS restraints |
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LS refinement shell |
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