+Open data
-Basic information
Entry | Database: PDB / ID: 8q7i | ||||||
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Title | PCNA from Chaetomium thermophilum in complex with Fen1 peptide | ||||||
Components |
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Keywords | REPLICATION / DNA clamp / DNA replication / homotrimer | ||||||
Function / homology | Function and homology information 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / PCNA complex / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / base-excision repair ...5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / PCNA complex / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / base-excision repair / Hydrolases; Acting on ester bonds / nucleolus / magnesium ion binding / mitochondrion / DNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Thermochaetoides thermophila DSM 1495 (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Alphey, M.S. / Wolford, C.B. / MacNeill, S.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Front Mol Biosci / Year: 2023 Title: Canonical binding of Chaetomium thermophilum DNA polymerase delta / zeta subunit PolD3 and flap endonuclease Fen1 to PCNA. Authors: Alphey, M.S. / Wolford, C.B. / MacNeill, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q7i.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q7i.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 8q7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q7i_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 8q7i_full_validation.pdf.gz | 426.3 KB | Display | |
Data in XML | 8q7i_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 8q7i_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/8q7i ftp://data.pdbj.org/pub/pdb/validation_reports/q7/8q7i | HTTPS FTP |
-Related structure data
Related structure data | 8p9oC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28813.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Some residues truncated or omitted from model due to flexibility Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / Gene: CTHT_0061010 / Plasmid: pEHISTEV-CtPCNA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 (pLysS) / References: UniProt: G0SF70 | ||||
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#2: Protein/peptide | Mass: 1662.928 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Some residues truncated or omitted from model due to flexibility Source: (synth.) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S2B5, Hydrolases; Acting on ester bonds | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 50mM Tris-HCl pH8.0, 150mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 20, 2023 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→21.86 Å / Num. obs: 23349 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Χ2: 0.98 / Net I/σ(I): 23.8 / Num. measured all: 247082 |
Reflection shell | Resolution: 1.95→2 Å / % possible obs: 99.7 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.182 / Num. measured all: 13994 / Num. unique obs: 1631 / CC1/2: 0.988 / Rpim(I) all: 0.065 / Rrim(I) all: 0.193 / Χ2: 1 / Net I/σ(I) obs: 11.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→21.86 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.861 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.971 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→21.86 Å
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