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- PDB-3f1w: Crystal structure of a mutant proliferating cell nuclear antigen ... -

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Basic information

Entry
Database: PDB / ID: 3f1w
TitleCrystal structure of a mutant proliferating cell nuclear antigen that blocks translesion synthesis
ComponentsProliferating cell nuclear antigen
KeywordsREPLICATION / DNA binding / DNA clamp / DNA damage / DNA repair / DNA replication / DNA-binding / 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 / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH ...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 / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / postreplication repair / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsFreudenthal, B.D. / Ramaswamy, S. / Washington, M.T.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of a Mutant Form of Proliferating Cell Nuclear Antigen That Blocks Translesion DNA Synthesis.
Authors: Freudenthal, B.D. / Ramaswamy, S. / Hingorani, M.M. / Washington, M.T.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)28,9741
Polymers28,9741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)86,9223
Polymers86,9223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Unit cell
Length a, b, c (Å)123.127, 123.127, 123.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28974.078 Da / Num. of mol.: 1 / Mutation: G178S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / 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: 5.368666 Å3/Da / Density % sol: 77.089279 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 2.06M ammonium sulfate, 0.1M Sodium citrate, pH 5.8, 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: 1.072 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 29, 2007 / Details: saggital focussing mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.9→29.86 Å / Num. all: 14067 / Num. obs: 14067 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 83 Å2 / Rsym value: 0.073 / Net I/σ(I): 14.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 11.01 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1510 / Rsym value: 0.605 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PLQ

1plq


Resolution: 2.901→19.974 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.255 816 5.95 %random
Rwork0.226 12901 --
obs0.228 13717 97.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.718 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso max: 148.6 Å2 / Biso mean: 77.786 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.901→19.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 0 0 1997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092004
X-RAY DIFFRACTIONf_angle_d1.2112709
X-RAY DIFFRACTIONf_chiral_restr0.079319
X-RAY DIFFRACTIONf_plane_restr0.004344
X-RAY DIFFRACTIONf_dihedral_angle_d18.314737
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.901-3.0820.3651330.322101223497
3.082-3.3190.3611370.32142227998
3.319-3.6510.2951330.2622113224698
3.651-4.1750.2551390.2312115225497
4.175-5.2440.2111340.1792163229798
5.244-19.9740.2191400.2052267240799

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