+Open data
-Basic information
Entry | Database: PDB / ID: 6tux | ||||||
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Title | human XPG-DNA, Complex 2 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / XPG nuclease domain bound to DNA | ||||||
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 / enzyme activator activity / transcription-coupled nucleotide-excision repair / 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 / enzyme activator activity / transcription-coupled nucleotide-excision repair / 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 / single-stranded DNA binding / chromosome / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 | 6tux.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tux.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 6tux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/6tux ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tux | HTTPS FTP |
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-Related structure data
Related structure data | 6turSC 6tusC 6tuwC 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: 40304.395 Da / Num. of mol.: 2 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 #2: DNA chain | Mass: 3364.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3358.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 2.55 Å3/Da / Density % sol: 51.76 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 5% PEG 3350, 50 mM Na Citrate pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.67 Å / Num. obs: 18419 / % possible obs: 99.9 % / Redundancy: 27.4 % / Biso Wilson estimate: 117.07 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3→3.107 Å / Num. unique obs: 3269 / CC1/2: 0.587 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TUR Resolution: 3.1→49.67 Å / SU ML: 0.403 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.934 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 145.28 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→49.67 Å
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Refine LS restraints |
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LS refinement shell |
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