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Yorodumi- PDB-6qh1: The structure of Schizosaccharomyces pombe PCNA in complex with a... -
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-Basic information
Entry | Database: PDB / ID: 6qh1 | ||||||
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Title | The structure of Schizosaccharomyces pombe PCNA in complex with an Spd1 derived peptide | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA repair / DNA replication / cell cycle regulation / PCNA-Spd1 complex | ||||||
Function / homology | Function and homology information mitotic DNA replication leading strand elongation / negative regulation of dCDP biosynthetic process / regulation of ribonucleoside-diphosphate reductase activity / ribonucleoside-diphosphate reductase inhibitor activity / : / Processive synthesis on the C-strand of the telomere / Telomere C-strand (Lagging Strand) Synthesis / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching / Removal of the Flap Intermediate ...mitotic DNA replication leading strand elongation / negative regulation of dCDP biosynthetic process / regulation of ribonucleoside-diphosphate reductase activity / ribonucleoside-diphosphate reductase inhibitor activity / : / Processive synthesis on the C-strand of the telomere / Telomere C-strand (Lagging Strand) Synthesis / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching / Removal of the Flap Intermediate / Processive synthesis on the lagging strand / chromatin => GO:0000785 / mitotic DNA replication lagging strand elongation / SUMOylation of DNA replication proteins / positive regulation of protein catabolic process => GO:0045732 / PCNA-Dependent Long Patch Base Excision Repair / Translesion synthesis by REV1 / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / protein localization => GO:0008104 / 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 / Removal of the Flap Intermediate from the C-strand / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cell cycle / positive regulation of DNA-directed DNA polymerase activity / PCNA complex / UV-damage excision repair / postreplication repair / DNA strand elongation involved in DNA replication / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / nuclear replication fork / error-prone translesion synthesis / mismatch repair / translesion synthesis / protein-membrane adaptor activity / site of double-strand break / cell division / protein-containing complex binding / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Kragelund, B.B. / Nielsen, O. / Olsen, J.G. / Kassem, N. / Prestel, A. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: To Be Published Title: The structure of Schizosaccharomyces pombe PCNA in complex with an Spd1 derived peptide Authors: Kragelund, B.B. / Olsen, J.G. / Kassem, N. / Prestel, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qh1.cif.gz | 153.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qh1.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qh1_validation.pdf.gz | 324.5 KB | Display | wwPDB validaton report |
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Full document | 6qh1_full_validation.pdf.gz | 344.7 KB | Display | |
Data in XML | 6qh1_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 6qh1_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/6qh1 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/6qh1 | HTTPS FTP |
-Related structure data
Related structure data | 3wgwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 28996.801 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: pcn1, pcn, SPBC16D10.09 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03392 #2: Protein/peptide | | Mass: 1050.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10585 |
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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: 2.17 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 100 mM TRIS-HCl pH 7.5, 18% (w/v) PEG4000 and 6% (v/v) glycerol, in the presence of 1.9 mM Spd1(27-46). [PCNA]=0.17 mM (5 mg/mL) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→75.7 Å / Num. obs: 19183 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.991 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.096 / Rpim(I) all: 0.552 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WGW Resolution: 2.9→75.68 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.911 / SU B: 27.551 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: 1 / Resolution: 2.9→75.68 Å
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Refine LS restraints |
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