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- PDB-6w9w: R80A PCNA mutant defective in BIR -

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Basic information

Entry
Database: PDB / ID: 6w9w
TitleR80A PCNA mutant defective in BIR
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / BIR / break induced replication / DNA repair / DNA damage / PCNA / proliferating cellular nuclear antigen
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 / 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
Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / :
Similarity search - Domain/homology
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRipley, B.M. / Washington, M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM081433-09 United States
CitationJournal: To be Published
Title: Structural analysis of PCNA mutant proteins defective in BIR, FF248-249AA and R80A
Authors: Ripley, B.M. / Washington, M.T.
History
DepositionMar 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)28,6471
Polymers28,6471
Non-polymers00
Water00
1
A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)85,9403
Polymers85,9403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Unit cell
Length a, b, c (Å)122.078, 122.078, 122.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28646.812 Da / Num. of mol.: 1 / Mutation: R80A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30, YBR088C, YBR0811 / Plasmid: pKW336
Details (production host): pET11a with 6His-tagged pol30 gene
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15873

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.29 Å3/Da / Density % sol: 76.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate, 0.2 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 14, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→54.595 Å / Num. obs: 34129 / % possible obs: 100 % / Redundancy: 21.3 % / Biso Wilson estimate: 65.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.026 / Rrim(I) all: 0.122 / Net I/σ(I): 27.6
Reflection shell

Rpim(I) all: 0.487 / Diffraction-ID: 1 / % possible all: 100 / Resolution: 2.65→2.72 Å

Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all
21.40.1131.622740.528
21.52.20851010.024

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Processing

Software
NameVersionClassification
Coot1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.5.14data scaling
Blu-Icedata extraction
pointlessphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PLQ

1plq


Resolution: 2.65→54.59 Å / SU ML: 0.4038 / Cross valid method: FREE R-VALUE / σ(F): 0.36 / Phase error: 28.3997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 1676 4.91 %
Rwork0.2141 32453 -
obs0.2156 34129 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.71 Å2
Refinement stepCycle: LAST / Resolution: 2.65→54.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 0 2010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272042
X-RAY DIFFRACTIONf_angle_d0.60562756
X-RAY DIFFRACTIONf_chiral_restr0.0441325
X-RAY DIFFRACTIONf_plane_restr0.0028353
X-RAY DIFFRACTIONf_dihedral_angle_d16.4295764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.730.36831290.34182691X-RAY DIFFRACTION100
2.73-2.820.39941030.31782765X-RAY DIFFRACTION100
2.82-2.920.44011140.29432710X-RAY DIFFRACTION100
2.92-3.030.2871660.27212685X-RAY DIFFRACTION100
3.03-3.170.31431220.25552704X-RAY DIFFRACTION100
3.17-3.340.25941180.23192747X-RAY DIFFRACTION100
3.34-3.550.31791400.2222708X-RAY DIFFRACTION100
3.55-3.820.24431920.21462658X-RAY DIFFRACTION100
3.82-4.20.24361640.20562682X-RAY DIFFRACTION99.89
4.21-4.810.22121520.16452685X-RAY DIFFRACTION100
4.82-6.060.16721300.20322705X-RAY DIFFRACTION100
6.07-54.590.20621460.19442713X-RAY DIFFRACTION99.76

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