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- PDB-4l60: Structure of C81R Mutant PCNA Protein Defective in Mismatch Repair -

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Basic information

Entry
Database: PDB / ID: 4l60
TitleStructure of C81R Mutant PCNA Protein Defective in Mismatch Repair
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA mismatch repair / DNA replication / Translesion synthesis / Nucleus
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: 3.003 Å
AuthorsWashington, T. / Boehm, E.
CitationJournal: Biochemistry / Year: 2013
Title: Distinct structural alterations in proliferating cell nuclear antigen block DNA mismatch repair.
Authors: Dieckman, L.M. / Boehm, E.M. / Hingorani, M.M. / Washington, M.T.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Sep 20, 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

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)28,7401
Polymers28,7401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.822, 121.822, 121.822
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: 28739.875 Da / Num. of mol.: 1 / Mutation: C81R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: POL30, YBR0811, YBR088C / Production host: Escherichia coli (E. coli) / 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: 5.24 Å3/Da / Density % sol: 76.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3000, 0.2M NaCl, and HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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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: Aug 3, 2012
RadiationMonochromator: RosenbaumRock monochromator double crystal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→21.5 Å / Num. all: 12279 / Num. obs: 12275 / % possible obs: 99.97 % / Observed criterion σ(I): 5 / Biso Wilson estimate: 105.82 Å2
Reflection shellResolution: 3→4.7536 Å / Redundancy: 19.9 % / Mean I/σ(I) obs: 9 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PLQ

1plq


Resolution: 3.003→21.5 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 29.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 589 4.8 %Random
Rwork0.1984 ---
obs0.2011 12275 99.97 %-
all-12279 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.003→21.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 0 0 2016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132046
X-RAY DIFFRACTIONf_angle_d1.5732759
X-RAY DIFFRACTIONf_dihedral_angle_d16.203772
X-RAY DIFFRACTIONf_chiral_restr0.088325
X-RAY DIFFRACTIONf_plane_restr0.005354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0027-3.30390.31361350.26552916X-RAY DIFFRACTION100
3.3039-3.77970.30311500.25142869X-RAY DIFFRACTION100
3.7797-4.75360.24611510.19742907X-RAY DIFFRACTION100
4.7536-21.53580.23591530.17562998X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 23.5407 Å / Origin y: 18.0317 Å / Origin z: -1.8117 Å
111213212223313233
T0.4797 Å20.1259 Å20.1015 Å2-0.8291 Å20.0991 Å2--0.5068 Å2
L4.0911 °23.9024 °22.0377 °2-7.7509 °23.4572 °2--5.0061 °2
S-0.1352 Å °0.5256 Å °0.0206 Å °-0.2736 Å °-0.1032 Å °0.0397 Å °-0.0313 Å °0.395 Å °0.2018 Å °
Refinement TLS groupSelection details: all

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