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- PDB-4l60: Structure of C81R Mutant PCNA Protein Defective in Mismatch Repair -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l60 | ||||||
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Title | Structure of C81R Mutant PCNA Protein Defective in Mismatch Repair | ||||||
![]() | Proliferating cell nuclear antigen | ||||||
![]() | DNA BINDING PROTEIN / DNA mismatch repair / DNA replication / Translesion synthesis / Nucleus | ||||||
Function / homology | ![]() Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH ...Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / postreplication repair / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / replication fork / positive regulation of DNA replication / nucleotide-excision repair / mitotic cell cycle / chromosome, telomeric region / DNA binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Washington, T. / Boehm, E. | ||||||
![]() | ![]() Title: Distinct structural alterations in proliferating cell nuclear antigen block DNA mismatch repair. Authors: Dieckman, L.M. / Boehm, E.M. / Hingorani, M.M. / Washington, M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.1 KB | Display | ![]() |
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PDB format | ![]() | 91.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.8 KB | Display | ![]() |
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Full document | ![]() | 431.8 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4l6pC ![]() 1plqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28739.875 Da / Num. of mol.: 1 / Mutation: C81R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: POL30, YBR0811, YBR088C / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.24 Å3/Da / Density % sol: 76.54 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3000, 0.2M NaCl, and HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: Aug 3, 2012 |
Radiation | Monochromator: RosenbaumRock monochromator double crystal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→21.5 Å / Num. all: 12279 / Num. obs: 12275 / % possible obs: 99.97 % / Observed criterion σ(I): 5 / Biso Wilson estimate: 105.82 Å2 |
Reflection shell | Resolution: 3→4.7536 Å / Redundancy: 19.9 % / Mean I/σ(I) obs: 9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PLQ Resolution: 3.003→21.5 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 29.34 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.003→21.5 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: 23.5407 Å / Origin y: 18.0317 Å / Origin z: -1.8117 Å
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Refinement TLS group | Selection details: all |