+Open data
-Basic information
Entry | Database: PDB / ID: 6tus | ||||||
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Title | human XPG, Apo2 form | ||||||
Components | (DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells) x 2 | ||||||
Keywords | DNA BINDING PROTEIN / XPG nuclease domain | ||||||
Function / homology | Function and homology information nucleotide-excision repair complex / base-excision repair, AP site formation / bubble DNA binding / regulation of catalytic activity / response to UV-C / RNA polymerase II complex binding / transcription-coupled nucleotide-excision repair / enzyme activator activity / response to UV / DNA endonuclease activity ...nucleotide-excision repair complex / base-excision repair, AP site formation / bubble DNA binding / regulation of catalytic activity / response to UV-C / RNA polymerase II complex binding / transcription-coupled nucleotide-excision repair / enzyme activator activity / response to UV / DNA endonuclease activity / nucleotide-excision repair / double-strand break repair via homologous recombination / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / chromosome / single-stranded DNA binding / double-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / protein-containing complex / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ruiz, F.M. / Fernandez-Tornero, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair. Authors: Gonzalez-Corrochano, R. / Ruiz, F.M. / Taylor, N.M.I. / Huecas, S. / Drakulic, S. / Spinola-Amilibia, M. / Fernandez-Tornero, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tus.cif.gz | 134.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tus.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 6tus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/6tus ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tus | HTTPS FTP |
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-Related structure data
Related structure data | 6turSC 6tuwC 6tuxC 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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Unit cell |
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-Components
#1: Protein | Mass: 40860.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC5, ERCM2, XPG, XPGC / Production host: Escherichia coli (E. coli) References: UniProt: P28715, Hydrolases; Acting on ester bonds | ||||||
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#2: Protein | Mass: 40789.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC5, ERCM2, XPG, XPGC / Production host: Escherichia coli (E. coli) References: UniProt: P28715, Hydrolases; Acting on ester bonds | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-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: 59.76 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 25% PEG 3350, 100 mM Bis-Tris pH 6.5, 200 mM Amm. Sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9787 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.85 Å / Num. obs: 35554 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 72.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.5→2.589 Å / Num. unique obs: 3887 / CC1/2: 0.439 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TUR Resolution: 2.5→47.85 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.91 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.81 Å2 / Biso mean: 82.0475 Å2 / Biso min: 43.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→47.85 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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