+Open data
-Basic information
Entry | Database: PDB / ID: 5y26 | ||||||
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Title | Crystal structure of native Dpb4-Dpb3 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Heterodimer / Histone fold complex / DNA binding / Epigenetic | ||||||
Function / homology | Function and homology information CMG complex assembly / DNA replication initiation / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER ...CMG complex assembly / DNA replication initiation / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / mitotic DNA replication initiation / leading strand elongation / nuclear replication fork / heterochromatin formation / chromatin DNA binding / DNA-templated DNA replication / protein heterodimerization activity / DNA damage response / chromatin / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å | ||||||
Authors | Chen, Y.H. / Li, Y. / Gao, F. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex. Authors: He, H. / Li, Y. / Dong, Q. / Chang, A.Y. / Gao, F. / Chi, Z. / Su, M. / Zhang, F. / Ban, H. / Martienssen, R. / Chen, Y.H. / Li, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y26.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y26.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y26_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 5y26_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 5y26_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 5y26_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/5y26 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/5y26 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27318.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: dpb4, SPBC3D6.09 Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others) References: UniProt: P87174, DNA-directed DNA polymerase |
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#2: Protein | Mass: 10540.134 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: SPCC16C4.22 Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others) References: UniProt: C6Y4D0 |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 27.92 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: PEG 3350, ches |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 16922 / % possible obs: 97.8 % / Redundancy: 15.1 % / Net I/σ(I): 27 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.661 / Num. unique obs: 1708 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.003→43.258 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.003→43.258 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -11.2517 Å / Origin y: 33.9877 Å / Origin z: 0.287 Å
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Refinement TLS group | Selection details: all |