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Yorodumi- PDB-3gpn: Structure of the non-trimeric form of the E113G PCNA mutant protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gpn | ||||||
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Title | Structure of the non-trimeric form of the E113G PCNA mutant protein | ||||||
Components | Proliferating cell nuclear antigen | ||||||
Keywords | DNA BINDING PROTEIN / Replication / DNA damage / DNA repair / DNA replication / DNA-binding / Isopeptide bond / Nucleus / Ubl conjugation | ||||||
Function / homology | Function and homology information Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / PCNA complex / establishment of mitotic sister chromatid cohesion ...Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / PCNA complex / establishment of mitotic sister chromatid cohesion / lagging strand elongation / postreplication repair / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / leading strand elongation / DNA polymerase processivity factor activity / error-free translesion synthesis / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA replication / positive regulation of DNA repair / replication fork / nucleotide-excision repair / mitotic cell cycle / chromosome, telomeric region / DNA binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Freudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions. Authors: Freudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gpn.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gpn.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/3gpn ftp://data.pdbj.org/pub/pdb/validation_reports/gp/3gpn | HTTPS FTP |
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-Related structure data
Related structure data | 3gpmC 1plqS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 28871.988 Da / Num. of mol.: 1 / Mutation: E113G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POL30, YBR0811, YBR088C / Plasmid: Pet11-a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P15873 |
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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: 3.97 Å3/Da / Density % sol: 68.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 1.6 M ammonium sulfate and 0.1 M sodium Citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Feb 4, 2008 / Details: saggital focusing mirrors |
Radiation | Monochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→81.38 Å / Num. all: 15940 / Num. obs: 14864 / % possible obs: 98.18 % / Redundancy: 4.75 % / Biso Wilson estimate: 42.619 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.5→2.565 Å / Redundancy: 4.75 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1041 / Rsym value: 0.365 / % possible all: 96.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PLQ Resolution: 2.5→81.38 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.022 / SU ML: 0.221 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.02 / ESU R: 0.32 / ESU R Free: 0.255 / 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: 42.619 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→81.38 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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