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- PDB-4yhr: Crystal Structure of Yeast Proliferating Cell Nuclear Antigen -

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Basic information

Entry
Database: PDB / ID: 4yhr
TitleCrystal Structure of Yeast Proliferating Cell Nuclear Antigen
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / replication fork / DNA-binding proteins / fungal proteins / proliferating cell nuclear antigen / Saccharomyces cerevisiae / crystallization / DNA repair / DNA replication / models / DNA sliding clamp / hydrophobic and hydrophilic interactions
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
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 / molecular replacement / Resolution: 2.9502 Å
AuthorsLitman, J.M. / Nguyen, V.Q. / Kondratick, C.M. / Powers, K.T. / Schnieders, M.J. / Washington, M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008365 United States
CitationJournal: To be published
Title: Dead-End Elimination with a Polarizable Force Field Repacks PCNA Models from Low-Resolution X-ray Diffraction into Atomic Resolution Structures
Authors: LuCore, S.D. / Litman, J.M. / Powers, K.T. / Lynn, A.M. / Tollefsen, W.T.A. / Fenn, T.D. / Washington, M.T. / Schnieders, M.J.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Database references / Refinement description / Category: citation / software / Item: _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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)30,0351
Polymers30,0351
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)90,1063
Polymers90,1063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)124.259, 124.259, 124.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
DetailsTrimer confirmed by extensive experimental evidence.

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 30035.320 Da / Num. of mol.: 1
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 / Plasmid: pET11a / 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: 5.32 Å3/Da / Density % sol: 76.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 15 mg/mL protein in 20 mM HEPES and 150 mM NaCL at pH 7.5. Crystallization solution: 2.2M ammonium sulfate, 0.2M ammonium fluoride. Hanging drop was 50% protein solution, ...Details: Protein solution: 15 mg/mL protein in 20 mM HEPES and 150 mM NaCL at pH 7.5. Crystallization solution: 2.2M ammonium sulfate, 0.2M ammonium fluoride. Hanging drop was 50% protein solution, 50% crystallization solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 21, 2013
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→37.47 Å / Num. obs: 13746 / % possible obs: 100 % / Redundancy: 21.82 % / Biso Wilson estimate: 122.12 Å2 / Rmerge(I) obs: 0.109 / Χ2: 1.16 / Net I/σ(I): 12.2 / Num. measured all: 302153 / Scaling rejects: 2268
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects
2.95-3.0622.260.8932.13028713581.3354
3.06-3.1822.130.8122.73065713711.35320
3.18-3.3222.230.72732984413391.3174
3.32-3.522.170.6153.63000913451.29188
3.5-3.72220.3587.33077513841.26323
3.72-422.040.3497.53034713691.22177
4-4.4121.770.17513.42983513581.12269
4.41-5.0421.710.09723.43016613800.9210
5.04-6.3521.590.08126.43025713900.88247
6.35-37.4720.370.0732.82997614520.96406

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREK9.9.9.5Ldata scaling
PHASER2.5.6phasing
PHENIX1.9refinement
PDB_EXTRACT3.15data extraction
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PLQ

1plq


Resolution: 2.9502→37.465 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 687 5.01 %
Rwork0.2464 13024 -
obs0.2477 13711 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 253.77 Å2 / Biso mean: 136.8029 Å2 / Biso min: 80.81 Å2
Refinement stepCycle: final / Resolution: 2.9502→37.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 0 0 2011
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042041
X-RAY DIFFRACTIONf_angle_d0.712753
X-RAY DIFFRACTIONf_chiral_restr0.025325
X-RAY DIFFRACTIONf_plane_restr0.003353
X-RAY DIFFRACTIONf_dihedral_angle_d12.302768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9502-3.17790.38171460.389925832729100
3.1779-3.49750.39591380.360325382676100
3.4975-4.00310.39621410.34522590273199
4.0031-5.04150.25621380.225825962734100
5.0415-37.46850.22051240.20927172841100

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