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- PDB-8gjf: afupcna bound with peptide mimetic -

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Basic information

Entry
Database: PDB / ID: 8gjf
Titleafupcna bound with peptide mimetic
Components
  • LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-PHE-TYR-HIS-SER-LYS-ARG
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / PCNA / DNA replication / peptide mimetic
Function / homology
Function and homology information


PCNA complex / lagging strand elongation / error-free translesion synthesis / myosin binding / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / endomembrane system / DNA binding / membrane
Similarity search - Function
Myosin-binding domain / Mysoin-binding motif of peroxisomes / 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 / :
Similarity search - Domain/homology
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVandborg, B. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Fungi / Year: 2023
Title: Towards a High-Affinity Peptidomimetic Targeting Proliferating Cell Nuclear Antigen from Aspergillus fumigatus.
Authors: Vandborg, B.C. / Horsfall, A.J. / Pederick, J.L. / Abell, A.D. / Bruning, J.B.
History
DepositionMar 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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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
D: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-PHE-TYR-HIS-SER-LYS-ARG
E: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-PHE-TYR-HIS-SER-LYS-ARG
F: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-PHE-TYR-HIS-SER-LYS-ARG


Theoretical massNumber of molelcules
Total (without water)90,0406
Polymers90,0406
Non-polymers00
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-48 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.004, 84.830, 70.452
Angle α, β, γ (deg.)90.00, 91.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-205-

HOH

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Components

#1: Protein Proliferating cell nuclear antigen


Mass: 28065.957 Da / Num. of mol.: 3 / Fragment: residues 614-869
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: CDV57_03149 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A229Y5V5
#2: Protein/peptide LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-PHE-TYR-HIS-SER-LYS-ARG


Mass: 1947.226 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Tacsimate pH 4.0, 0.1M Na Acetate, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2022 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→42.2 Å / Num. obs: 57623 / % possible obs: 99.2 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.033 / Rrim(I) all: 0.088 / Χ2: 1.04 / Net I/σ(I): 13 / Num. measured all: 405868
Reflection shellResolution: 2→2.05 Å / % possible obs: 99.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.331 / Num. measured all: 30633 / Num. unique obs: 4252 / CC1/2: 0.609 / Rpim(I) all: 0.527 / Rrim(I) all: 1.433 / Χ2: 1.01 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.2 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2703 2888 5.01 %
Rwork0.2326 --
obs0.2345 57608 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5957 0 0 421 6378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056048
X-RAY DIFFRACTIONf_angle_d1.1968206
X-RAY DIFFRACTIONf_dihedral_angle_d16.112850
X-RAY DIFFRACTIONf_chiral_restr0.0541008
X-RAY DIFFRACTIONf_plane_restr0.0071052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.40591170.35662600X-RAY DIFFRACTION99
2.03-2.070.3561310.32962630X-RAY DIFFRACTION99
2.07-2.110.34851400.32032573X-RAY DIFFRACTION100
2.11-2.150.31381620.3052576X-RAY DIFFRACTION99
2.15-2.190.29051400.29012605X-RAY DIFFRACTION100
2.19-2.240.33121480.29642584X-RAY DIFFRACTION99
2.24-2.290.32011310.29692626X-RAY DIFFRACTION99
2.29-2.350.37411350.29932628X-RAY DIFFRACTION100
2.35-2.410.28741550.2812567X-RAY DIFFRACTION99
2.41-2.480.33311070.28362629X-RAY DIFFRACTION99
2.48-2.560.29831120.27692636X-RAY DIFFRACTION99
2.56-2.650.30641480.28012497X-RAY DIFFRACTION96
2.65-2.760.32661340.26872530X-RAY DIFFRACTION97
2.76-2.880.31831550.27312599X-RAY DIFFRACTION100
2.88-3.040.30761490.26922633X-RAY DIFFRACTION100
3.04-3.230.26421550.25252621X-RAY DIFFRACTION100
3.23-3.480.2531570.22832605X-RAY DIFFRACTION100
3.48-3.820.24651260.20562645X-RAY DIFFRACTION100
3.83-4.380.22861220.18922653X-RAY DIFFRACTION100
4.38-5.510.20581200.16982579X-RAY DIFFRACTION96
5.51-42.20.24761440.20082704X-RAY DIFFRACTION100

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