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Yorodumi- PDB-5xyn: The crystal structure of Csm2-Psy3-Shu1-Shu2 complex from budding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xyn | ||||||||||||
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Title | The crystal structure of Csm2-Psy3-Shu1-Shu2 complex from budding yeast | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Comlex / REPLICATION | ||||||||||||
Function / homology | Function and homology information positive regulation of single-strand break repair via homologous recombination / Shu complex / error-free postreplication DNA repair / meiotic chromosome segregation / maintenance of rDNA / DNA recombinase assembly / recombinational repair / error-free translesion synthesis / site of double-strand break / nucleolus ...positive regulation of single-strand break repair via homologous recombination / Shu complex / error-free postreplication DNA repair / meiotic chromosome segregation / maintenance of rDNA / DNA recombinase assembly / recombinational repair / error-free translesion synthesis / site of double-strand break / nucleolus / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å | ||||||||||||
Authors | Zhang, S. / Zhang, T. / Ding, J. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Structural basis for the functional role of the Shu complex in homologous recombination. Authors: Zhang, S. / Wang, L. / Tao, Y. / Bai, T. / Lu, R. / Zhang, T. / Chen, J. / Ding, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xyn.cif.gz | 164.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xyn.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 5xyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xyn_validation.pdf.gz | 457.2 KB | Display | wwPDB validaton report |
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Full document | 5xyn_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 5xyn_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5xyn_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xyn ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xyn | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28427.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: PSY3, YLR376C, L8039.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12318 |
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#2: Protein | Mass: 24983.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CSM2, YIL132C / Production host: Escherichia coli (E. coli) / References: UniProt: P40465 |
#3: Protein | Mass: 17138.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SHU1, YHL006C / Production host: Escherichia coli (E. coli) / References: UniProt: P38751 |
#4: Protein | Mass: 26152.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SHU2, YDR078C, D4436 / Production host: Escherichia coli (E. coli) / References: UniProt: P38957 |
#5: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.53 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis-Tris, pH 6.5, 0.2M potassium sodium tartrate, 10% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 9, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→50 Å / Num. obs: 24375 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.01 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Χ2: 0.924 / Net I/σ(I): 5.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: SAD / Resolution: 3.3→44.33 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.865 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.731 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→44.33 Å
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Refine LS restraints |
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