+Open data
-Basic information
Entry | Database: PDB / ID: 6j0w | ||||||
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Title | Crystal Structure of Yeast Rtt107 and Nse6 | ||||||
Components |
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Keywords | PROTEIN BINDING / BRCT domain / mitosis / protein interaction | ||||||
Function / homology | Function and homology information regulation of DNA double-strand break processing / Smc5-Smc6 complex / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / retrotransposon silencing / ATPase inhibitor activity / regulation of DNA damage checkpoint / chromatin looping / regulation of telomere maintenance / protein sumoylation ...regulation of DNA double-strand break processing / Smc5-Smc6 complex / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / retrotransposon silencing / ATPase inhibitor activity / regulation of DNA damage checkpoint / chromatin looping / regulation of telomere maintenance / protein sumoylation / cell periphery / double-strand break repair via homologous recombination / double-strand break repair / nucleosome assembly / chromosome, telomeric region / DNA repair / chromatin binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wan, B. / Wu, J. / Lei, M. | ||||||
Citation | Journal: Mol.Cell / Year: 2019 Title: Molecular Basis for Control of Diverse Genome Stability Factors by the Multi-BRCT Scaffold Rtt107. Authors: Wan, B. / Wu, J. / Meng, X. / Lei, M. / Zhao, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j0w.cif.gz | 401.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j0w.ent.gz | 331.2 KB | Display | PDB format |
PDBx/mmJSON format | 6j0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0w ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0w | HTTPS FTP |
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-Related structure data
Related structure data | 6j0vSC 6j0xC 6j0yC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 59359.969 Da / Num. of mol.: 2 / Fragment: NTD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RTT107, ESC4, YHR154W / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38850 #2: Protein/peptide | Mass: 3161.279 Da / Num. of mol.: 2 / Fragment: Rtt107 interacting motif Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: KRE29, YER038C / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40026 #3: Water | ChemComp-HOH / | |
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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: 2.39 Å3/Da / Density % sol: 48.5 % / Mosaicity: 0.18 ° |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 6 Details: 22% PEG 3350, 0.1M Bis-Tris pH 6.0, 0.2M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97855 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 30, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97855 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→82.05 Å / Num. obs: 46118 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 41.97 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.052 / Rrim(I) all: 0.1 / Net I/σ(I): 12.1 / Num. measured all: 173636 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J0V Resolution: 2.4→45.707 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 30.35 / 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: 124.82 Å2 / Biso mean: 48.8934 Å2 / Biso min: 9.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→45.707 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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