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- PDB-4l6p: Structure of C22Y Mutant PCNA protein defective in DNA mismatch repair -

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Basic information

Entry
Database: PDB / ID: 4l6p
TitleStructure of C22Y Mutant PCNA protein defective in DNA mismatch repair
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA mismatch repair / DNA replication / translesion synthesis / Ubiquitylation / SUMOylation / Nucleus
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 S288c (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.68 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 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2May 27, 2015Group: Structure summary
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6835
Polymers89,4993
Non-polymers1842
Water1,31573
1
A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)29,8331
Polymers29,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)29,8331
Polymers29,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0173
Polymers29,8331
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.941, 90.619, 140.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 29832.959 Da / Num. of mol.: 3 / Mutation: C22Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: POL30, YBR0811, YBR088C / Production host: Escherichia coli (E. coli) / References: UniProt: P15873
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M AmSO4, 0.2M Lithium Sulfate Monohydrate, 0.1M Sodium Cacodylate Trihydrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Osmic Blue
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→20.914 Å / Num. obs: 31494 / % possible obs: 100 % / Observed criterion σ(I): 5
Reflection shellResolution: 2.68→2.78 Å / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata 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: 2.68→20.914 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 1589 5.05 %
Rwork0.2099 --
obs0.2134 31435 99.94 %
all-31435 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→20.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5967 0 12 73 6052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016071
X-RAY DIFFRACTIONf_angle_d1.338187
X-RAY DIFFRACTIONf_dihedral_angle_d13.2052265
X-RAY DIFFRACTIONf_chiral_restr0.055965
X-RAY DIFFRACTIONf_plane_restr0.0071042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.76640.38651470.32042664X-RAY DIFFRACTION100
2.7664-2.8650.37741320.29362689X-RAY DIFFRACTION100
2.865-2.97940.34831410.28022678X-RAY DIFFRACTION100
2.9794-3.11460.3331590.27012659X-RAY DIFFRACTION100
3.1146-3.27820.41041450.27432681X-RAY DIFFRACTION100
3.2782-3.48270.3511390.2662708X-RAY DIFFRACTION100
3.4827-3.75020.3161430.23092700X-RAY DIFFRACTION100
3.7502-4.1250.28741410.2052704X-RAY DIFFRACTION100
4.125-4.71590.19551350.14872740X-RAY DIFFRACTION100
4.7159-5.91910.21591710.16982729X-RAY DIFFRACTION100
5.9191-20.91490.25241360.18712894X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.8173 Å / Origin y: -6.8069 Å / Origin z: 20.1368 Å
111213212223313233
T0.3064 Å2-0.0339 Å2-0.0243 Å2-0.2814 Å20.0236 Å2--0.2561 Å2
L1.2224 °2-0.2 °20.2269 °2-0.2955 °20.1085 °2--0.3016 °2
S-0.02 Å °-0.1064 Å °-0.1126 Å °-0.035 Å °0.0196 Å °0.0075 Å °0.014 Å °-0.0431 Å °-0.0018 Å °
Refinement TLS groupSelection details: all

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