+Open data
-Basic information
Entry | Database: PDB / ID: 3wtd | ||||||
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Title | Structure of PAXX | ||||||
Components | Uncharacterized protein C9orf142 | ||||||
Keywords | NUCLEAR PROTEIN / DNA repair / Scaffold | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ochi, T. / Blundell, T.L. | ||||||
Citation | Journal: Science / Year: 2015 Title: DNA repair. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair. Authors: Ochi, T. / Blackford, A.N. / Coates, J. / Jhujh, S. / Mehmood, S. / Tamura, N. / Travers, J. / Wu, Q. / Draviam, V.M. / Robinson, C.V. / Blundell, T.L. / Jackson, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wtd.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wtd.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wtd_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
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Full document | 3wtd_full_validation.pdf.gz | 432.6 KB | Display | |
Data in XML | 3wtd_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 3wtd_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/3wtd ftp://data.pdbj.org/pub/pdb/validation_reports/wt/3wtd | HTTPS FTP |
-Related 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: 17853.162 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP RESIDUES 1-166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C9orf142 / Plasmid: pHAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q9BUH6 #2: 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: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5M ammonium sulfate, 12%(v/v) glycerol, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2013 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→55.2 Å / Num. obs: 16230 / % possible obs: 98.5 % / Redundancy: 9.6 % / Rsym value: 0.052 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 10 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.627 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→45.974 Å / SU ML: 0.26 / σ(F): 1.36 / Phase error: 23.93 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→45.974 Å
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Refine LS restraints |
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LS refinement shell |
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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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