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- PDB-3l0x: Structure of split yeast PCNA -

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Basic information

Entry
Database: PDB / ID: 3l0x
TitleStructure of split yeast PCNA
Components(Proliferating cell nuclear antigen) x 2
KeywordsREPLICATION / DNA damage / DNA repair / DNA replication / DNA-binding / Isopeptide bond / Nucleus / Ubl conjugation
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
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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 ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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 / : / Roll / 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 Å
AuthorsFreudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange.
Authors: Freudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)29,6622
Polymers29,6622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-41 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.999, 122.999, 122.999
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: 19238.893 Da / Num. of mol.: 1 / Fragment: N fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30, YBR0811, YBR088C / Plasmid: petduet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15873
#2: Protein Proliferating cell nuclear antigen / PCNA


Mass: 10422.843 Da / Num. of mol.: 1 / Fragment: C fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30, YBR0811, YBR088C / Plasmid: petduet-1 / Production host: Escherichia coli (E. coli) / 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: 5.23 Å3/Da / Density % sol: 76.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.9M ammonium sulfate, 0.1M sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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 25, 2009 / Details: sagitally focusing mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→86.97 Å / Num. all: 12666 / Num. obs: 12666 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 89.474 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.1 Å / Redundancy: 6.99 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1197 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PLQ

1plq


Resolution: 3→43.5 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.219 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.52 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.267 615 4.9 %RANDOM
Rwork0.243 ---
all0.244 12666 --
obs0.244 12643 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 123.09 Å2 / Biso mean: 89.474 Å2 / Biso min: 62.15 Å2
Refinement stepCycle: LAST / Resolution: 3→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 0 0 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222023
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9922728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42825.61889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69315382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.633158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211475
X-RAY DIFFRACTIONr_mcbond_it0.5521.51264
X-RAY DIFFRACTIONr_mcangle_it1.03722050
X-RAY DIFFRACTIONr_scbond_it0.9823759
X-RAY DIFFRACTIONr_scangle_it1.8114.5678
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 37 -
Rwork0.348 877 -
all-914 -
obs-1197 99.89 %

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