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- PDB-6d0r: Structure of a DNA retention-prone PCNA variant -

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Basic information

Entry
Database: PDB / ID: 6d0r
TitleStructure of a DNA retention-prone PCNA variant
ComponentsProliferating cell nuclear antigen
KeywordsREPLICATION / Mutant / DNA
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 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
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / : / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85856959127 Å
AuthorsKelch, B.A. / Gaubitz, C.
Funding support United States, 2items
OrganizationGrant numberCountry
American Cancer Society440685 United States
Swiss National Science Foundation168972 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Effective mismatch repair depends on timely control of PCNA retention on DNA by the Elg1 complex.
Authors: Paul Solomon Devakumar, L.J. / Gaubitz, C. / Lundblad, V. / Kelch, B.A. / Kubota, T.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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)29,5401
Polymers29,5401
Non-polymers00
Water0
1
A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)88,6193
Polymers88,6193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area3800 Å2
ΔGint-19 kcal/mol
Surface area36280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.716, 121.716, 121.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

#1: Protein Proliferating cell nuclear antigen / / PCNA


Mass: 29539.807 Da / Num. of mol.: 1 / Mutation: D17K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: POL30, YBR088C, YBR0811 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 5.06 Å3/Da / Density % sol: 75.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50 mM sodium citrate pH 5.3 and 1.7 M (NH4)2SO4 / Temp details: RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14213 / % possible obs: 100 % / Redundancy: 20.8 % / Biso Wilson estimate: 55.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.033 / Rrim(I) all: 0.149 / Χ2: 1.009 / Net I/σ(I): 25.99
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 18.8 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 707 / CC1/2: 0.858 / Rpim(I) all: 0.256 / Rrim(I) all: 1.102 / Χ2: 0.866 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootv0.8.8model building
PHENIX1.12-2829refinement
PHASERphasing
HKL-3000data reduction
HKL-3000v703xdata scaling
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHR

4yhr


Resolution: 2.85856959127→38.4899787685 Å / SU ML: 0.351662319592 / Cross valid method: FREE R-VALUE / σ(F): 1.33473444407 / Phase error: 31.202435993
RfactorNum. reflection% reflectionSelection details
Rfree0.275881391497 689 5.06208213945 %Random selection
Rwork0.242032540516 ---
obs0.243790221328 13611 95.8993870218 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.5193499882 Å2
Refinement stepCycle: LAST / Resolution: 2.85856959127→38.4899787685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 0 0 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006040310186332042
X-RAY DIFFRACTIONf_angle_d0.832652601192753
X-RAY DIFFRACTIONf_chiral_restr0.0485084592907325
X-RAY DIFFRACTIONf_plane_restr0.00491871153937352
X-RAY DIFFRACTIONf_dihedral_angle_d3.318388427691258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8586-3.07920.3733836721581380.3166155942692660X-RAY DIFFRACTION99.9285714286
3.0792-3.38890.3444031625081430.3049289889892603X-RAY DIFFRACTION97.792022792
3.3889-3.87890.3360804428321300.2785916020562396X-RAY DIFFRACTION89.5109851169
3.8789-4.88540.2260134620441290.2040053928982509X-RAY DIFFRACTION93.0183356841
4.8854-38.49340.2345946546781490.2121255092042754X-RAY DIFFRACTION99.1800478305

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