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- PDB-5dai: Proliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide -

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Basic information

Entry
Database: PDB / ID: 5dai
TitleProliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide
Components
  • C-terminus of FEN-1 protein
  • DNA polymerase sliding clamp 1
KeywordsTRANSFERASE / complex / PIP box binder
Function / homology
Function and homology information


5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding / identical protein binding
Similarity search - Function
Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 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 / PIN-like domain superfamily / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp 1 / Flap endonuclease 1
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
Thermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLadner, J.E. / Altieri, A.S. / Kelman, Z.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp.
Authors: Altieri, A.S. / Ladner, J.E. / Li, Z. / Robinson, H. / Sallman, Z.F. / Marino, J.P. / Kelman, Z.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase sliding clamp 1
B: C-terminus of FEN-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,56713
Polymers30,5102
Non-polymers1,05711
Water1,76598
1
A: DNA polymerase sliding clamp 1
B: C-terminus of FEN-1 protein
hetero molecules

A: DNA polymerase sliding clamp 1
B: C-terminus of FEN-1 protein
hetero molecules

A: DNA polymerase sliding clamp 1
B: C-terminus of FEN-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,70039
Polymers91,5306
Non-polymers3,17033
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13350 Å2
ΔGint-419 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.070, 152.070, 35.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein DNA polymerase sliding clamp 1 / Proliferating cell nuclear antigen homolog 1 / PCNA 1


Mass: 29099.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: pcn1, TK0535 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JF32
#2: Protein/peptide C-terminus of FEN-1 protein


Mass: 1410.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermococcus kodakarensis KOD1 (archaea) / References: UniProt: Q5JGN0*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: Well solution: 2.8 M ammonium sulfate, 100 mM citric acid buffer pH 5.3, and 10% PEG 4000.
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→28.8 Å / Num. obs: 20143 / % possible obs: 98.2 % / Redundancy: 3.31 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LX1

3lx1


Resolution: 2→28.762 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1025 5.09 %random
Rwork0.1815 ---
obs0.1835 20133 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 55 98 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082198
X-RAY DIFFRACTIONf_angle_d1.1362969
X-RAY DIFFRACTIONf_dihedral_angle_d14.834842
X-RAY DIFFRACTIONf_chiral_restr0.046329
X-RAY DIFFRACTIONf_plane_restr0.004379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.10560.33071520.27352770X-RAY DIFFRACTION100
2.1056-2.23750.3221480.23472753X-RAY DIFFRACTION100
2.2375-2.41010.31671430.23432783X-RAY DIFFRACTION99
2.4101-2.65250.31461490.22812733X-RAY DIFFRACTION99
2.6525-3.0360.32171620.21442738X-RAY DIFFRACTION98
3.036-3.82360.19281490.16592701X-RAY DIFFRACTION97
3.8236-28.76470.15751220.14992630X-RAY DIFFRACTION94

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