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- PDB-6wac: FF248-249AA PCNA mutant defective in BIR -

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Basic information

Entry
Database: PDB / ID: 6wac
TitleFF248-249AA 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 / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / Translesion synthesis by REV1 ...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 / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / PCNA complex / Translesion Synthesis by POLH / establishment of mitotic sister chromatid cohesion / Termination of translesion DNA synthesis / lagging strand elongation / postreplication repair / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / leading strand elongation / DNA polymerase processivity factor activity / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / 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
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: 2.9 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 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 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)28,1571
Polymers28,1571
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)84,4723
Polymers84,4723
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3950 Å2
ΔGint-16 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.881, 86.881, 100.724
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28157.271 Da / Num. of mol.: 1 / Mutation: F248A, F249A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30, YBR088C, YBR0811 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium chloride hexahydrate, sodium dimethylarsinic acid, PEG1000

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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: Apr 15, 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: 2.9→60.28 Å / Num. obs: 12383 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 82.02 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.057 / Net I/σ(I): 13.4
Reflection shellResolution: 2.9→3.003 Å / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 2 / Num. unique obs: 595 / Rpim(I) all: 0.604

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Processing

Software
NameVersionClassification
Coot0.8.8refinement
PHENIX1.17.1_3660refinement
TRUNCATEdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PLQ

1plq


Resolution: 2.9→60.28 Å / SU ML: 0.4998 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 33.259
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2701 594 4.8 %
Rwork0.2366 11789 -
obs0.2383 12383 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→60.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 0 0 1972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261999
X-RAY DIFFRACTIONf_angle_d0.53232697
X-RAY DIFFRACTIONf_chiral_restr0.0434322
X-RAY DIFFRACTIONf_plane_restr0.0039345
X-RAY DIFFRACTIONf_dihedral_angle_d16.9145755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.190.41241320.36542945X-RAY DIFFRACTION97.99
3.19-3.650.34031860.27732924X-RAY DIFFRACTION99.11
3.65-4.60.2631250.23522983X-RAY DIFFRACTION98.42
4.6-60.280.22011510.20242937X-RAY DIFFRACTION98.22

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