[English] 日本語
![](img/lk-miru.gif)
- PDB-6ug1: Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ug1 | ||||||
---|---|---|---|---|---|---|---|
Title | Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN/DNA / DNA damage recognition / DNA repair / Beta-hairpin motif / xeroderma pigmentosum / XPC / Rad4 / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / ubiquitin-dependent glycoprotein ERAD pathway / XPC complex / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding ...PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / ubiquitin-dependent glycoprotein ERAD pathway / XPC complex / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair / ERAD pathway / ubiquitin binding / nucleotide-excision repair / protein-macromolecule adaptor activity / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Paul, D. / Min, J.-H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex. Authors: Paul, D. / Mu, H. / Tavakoli, A. / Dai, Q. / Chakraborty, S. / He, C. / Ansari, A. / Broyde, S. / Min, J.H. #1: ![]() Title: Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Authors: Chen, X. / Velmurugu, Y. / Zheng, G. / Park, B. / Shim, Y. / Kim, Y. / Liu, L. / Van Houten, B. / He, C. / Ansari, A. / Min, J.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 252.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 207.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 478.9 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 33.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 58978.613 Da / Num. of mol.: 1 / Fragment: UNP residues 129-632 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RAD4, YER162C / Production host: ![]() |
---|---|
#2: Protein | Mass: 6192.080 Da / Num. of mol.: 1 / Fragment: UNP residues 256-311 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RAD23, YEL037C, SYGP-ORF29 / Production host: ![]() |
#3: DNA chain | Mass: 6504.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: DNA chain | Mass: 6444.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.14 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 18202 / % possible obs: 91.2 % / Redundancy: 2.9 % / CC1/2: 0.744 / Net I/σ(I): 17.35 |
Reflection shell | Highest resolution: 2.8 Å / Num. unique obs: 18202 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 224.48 Å2 / Biso mean: 84.1836 Å2 / Biso min: 17.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.833→39.412 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|