+Open data
-Basic information
Entry | Database: PDB / ID: 6tuw | ||||||
---|---|---|---|---|---|---|---|
Title | human XPG-DNA, Complex 1 | ||||||
Components |
| ||||||
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 / transcription-coupled nucleotide-excision repair / response to UV / enzyme activator activity / 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 / response to UV / enzyme activator activity / 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 / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tuw.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tuw.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 6tuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tuw_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6tuw_full_validation.pdf.gz | 451.5 KB | Display | |
Data in XML | 6tuw_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6tuw_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/6tuw ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tuw | HTTPS FTP |
-Related structure data
Related structure data | 6turSC 6tusC 6tuxC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: 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 |
---|---|
#2: DNA chain | Mass: 3364.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
#3: DNA chain | Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.05 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→45.79 Å / Num. obs: 6627 / % possible obs: 99.8 % / Redundancy: 15.9 % / Biso Wilson estimate: 145.35 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 3.5→3.625 Å / Num. unique obs: 1536 / CC1/2: 0.827 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TUR Resolution: 3.5→45.79 Å / SU ML: 0.3407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.6614
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 212.3 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→45.79 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell |
|