+Open data
-Basic information
Entry | Database: PDB / ID: 5y27 | ||||||
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Title | Crystal structure of Se-Met Dpb4-Dpb3 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / heterodimer / histone fold complex / DNA binging / 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 / SAD / Resolution: 1.9 Å | ||||||
Authors | Li, Y. / Gao, F. / Su, M. / Zhang, F.B. / Chen, Y.H. | ||||||
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 | 5y27.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y27.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 5y27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y27_validation.pdf.gz | 448.3 KB | Display | wwPDB validaton report |
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Full document | 5y27_full_validation.pdf.gz | 449.8 KB | Display | |
Data in XML | 5y27_validation.xml.gz | 12 KB | Display | |
Data in CIF | 5y27_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/5y27 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/5y27 | 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: 27506.492 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: 10587.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission 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: 2.87 Å3/Da / Density % sol: 57.12 % Preparation: The Solvent content/Matthews coefficient are the deposited values. Because the residues of A 107-240 had been degraded in the crystal. |
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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: 0.97915 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: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 20156 / % possible obs: 100 % / Redundancy: 49.9 % / Net I/σ(I): 72 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 50 % / Rmerge(I) obs: 0.713 / Num. unique obs: 2032 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→37.365 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→37.365 Å
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Refine LS restraints |
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LS refinement shell |
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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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