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- PDB-6cx4: V180A Mutant of Yeast PCNA -

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Basic information

Entry
Database: PDB / ID: 6cx4
TitleV180A Mutant of Yeast PCNA
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA Replication / DNA Repair / DNA Recombination Scaffold
Function / homology
Function and homology information


positive regulation of DNA metabolic process / 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 / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 ...positive regulation of DNA metabolic process / 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 / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / DNA damage tolerance / 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 / translesion synthesis / subtelomeric heterochromatin formation / mismatch repair / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.081 Å
AuthorsPowers, K.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)TGM081433 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108027 United States
CitationJournal: PLoS ONE / Year: 2016
Title: Identification of New Mutations at the PCNA Subunit Interface that Block Translesion Synthesis.
Authors: Kondratick, C.M. / Boehm, E.M. / Dieckman, L.M. / Powers, K.T. / Sanchez, J.C. / Mueting, S.R. / Washington, M.T.
History
DepositionApr 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 7, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
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)29,0541
Polymers29,0541
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)87,1623
Polymers87,1623
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)122.555, 122.555, 122.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 29054.145 Da / Num. of mol.: 1 / Mutation: V180A
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 / Variant: S288c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): 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: 5.37 Å3/Da / Density % sol: 77.09 % / Description: Regular Cube
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop
Details: 2.2M Ammonium Sulfate 0.2M Potassium Chloride 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 15, 2013
RadiationMonochromator: Rosenbaum-Rock Si(111) saggitally focused mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.08→24.51 Å / Num. obs: 11585 / % possible obs: 100 % / Redundancy: 8.56 % / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.116 / Χ2: 1.16 / Net I/σ(I): 9.3 / Num. measured all: 99880 / Scaling rejects: 750
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
3.08-3.198.810.72211500.7651.28100
3.19-3.328.760.6282.511370.6681.36100
3.32-3.478.750.5113.111560.5441.31100
3.47-3.658.750.411411160.4361.31100
3.65-3.888.710.3175.211610.3371.27100
3.88-4.188.640.2456.411470.2611.24100
4.18-4.68.520.1310.911520.1391.0599.9
4.6-5.258.480.114.211750.1070.96100
5.25-6.68.380.08117.511630.0860.92100
6.6-24.517.830.04728.612280.0510.88100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
Blu-Icedata collection
Coot0.8.6.1model building
PHENIX1.11.1-2575refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PLQ

1plq


Resolution: 3.081→24.51 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 0.77 / Phase error: 33.01
RfactorNum. reflection% reflection
Rfree0.2666 1046 4.76 %
Rwork0.2463 --
obs0.2473 21962 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 231.39 Å2 / Biso mean: 153.7623 Å2 / Biso min: 113.02 Å2
Refinement stepCycle: final / Resolution: 3.081→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 0 1996
Num. residues----255

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