+Open data
-Basic information
Entry | Database: PDB / ID: 3t7k | ||||||
---|---|---|---|---|---|---|---|
Title | Complex structure of Rtt107p and phosphorylated histone H2A | ||||||
Components |
| ||||||
Keywords | PROTEIN BINDING / BRCT / DNA repair / phospho-peptide | ||||||
Function / homology | Function and homology information regulation of DNA double-strand break processing / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / Condensation of Prophase Chromosomes / retrotransposon silencing / regulation of DNA damage checkpoint / replication fork protection complex / RMTs methylate histone arginines / cell periphery / nucleosome assembly ...regulation of DNA double-strand break processing / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / Condensation of Prophase Chromosomes / retrotransposon silencing / regulation of DNA damage checkpoint / replication fork protection complex / RMTs methylate histone arginines / cell periphery / nucleosome assembly / structural constituent of chromatin / double-strand break repair / nucleosome / chromatin organization / protein heterodimerization activity / DNA repair / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.028 Å | ||||||
Authors | Li, X. / Li, F. / Wu, J. / Shi, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structure of C-terminal Tandem BRCT Repeats of Rtt107 Protein Reveals Critical Role in Interaction with Phosphorylated Histone H2A during DNA Damage Repair Authors: Li, X. / Liu, K. / Li, F. / Wang, J. / Huang, H. / Wu, J. / Shi, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3t7k.cif.gz | 108 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3t7k.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 3t7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/3t7k ftp://data.pdbj.org/pub/pdb/validation_reports/t7/3t7k | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29388.227 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RTT107 / Production host: Escherichia coli (E. coli) / References: UniProt: P38850 #2: Protein/peptide | Mass: 927.912 Da / Num. of mol.: 2 / Fragment: phosphorylated C-terminal peptide / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04911 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.62 % / Mosaicity: 7.234 ° |
---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 14%(w/v) PEG 1500, 0.2M NaCl, 0.1M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.9 % / Av σ(I) over netI: 11.69 / Number: 116925 / Rmerge(I) obs: 0.076 / Χ2: 1.17 / D res high: 2.03 Å / D res low: 50 Å / Num. obs: 39702 / % possible obs: 96.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.028→50 Å / Num. all: 41142 / Num. obs: 39702 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 33.71 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.173 / Net I/σ(I): 8.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.028→30.548 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7501 / SU ML: 0.28 / σ(F): 0.08 / Phase error: 31.69 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.999 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.27 Å2 / Biso mean: 44.6295 Å2 / Biso min: 24.79 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.028→30.548 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|