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- PDB-5da7: monomeric PCNA bound to a small protein inhibitor -

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Basic information

Entry
Database: PDB / ID: 5da7
Titlemonomeric PCNA bound to a small protein inhibitor
Components
  • DNA polymerase sliding clamp 1, Proliferating cell nuclear antigen
  • Thermococcales inhibitor of PCNA
KeywordsDNA binding protein/inhibitor / complex / inhibitor / DNA binding protein-inhibitor complex
Function / homology
Function and homology information


DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA binding / identical protein binding
Similarity search - Function
: / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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, 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
DNA polymerase sliding clamp 1 / PCNA-inhibitor
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 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 19, 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

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Assembly

Deposited unit
A: DNA polymerase sliding clamp 1, Proliferating cell nuclear antigen
D: DNA polymerase sliding clamp 1, Proliferating cell nuclear antigen
B: Thermococcales inhibitor of PCNA
E: Thermococcales inhibitor of PCNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,18822
Polymers73,4594
Non-polymers1,72918
Water00
1
A: DNA polymerase sliding clamp 1, Proliferating cell nuclear antigen
B: Thermococcales inhibitor of PCNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,88214
Polymers36,7292
Non-polymers1,15312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-148 kcal/mol
Surface area13760 Å2
MethodPISA
2
D: DNA polymerase sliding clamp 1, Proliferating cell nuclear antigen
E: Thermococcales inhibitor of PCNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3068
Polymers36,7292
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-106 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.341, 184.079, 330.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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


Mass: 29099.311 Da / Num. of mol.: 2
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 Thermococcales inhibitor of PCNA


Mass: 7629.947 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
References: UniProt: Q5JH72
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Well solution: 1.2 M ammonium sulfate, 50 mM sodium citrate buffer, and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2014
RadiationMonochromator: coated mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 30707 / % possible obs: 98.9 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 36.6
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.892

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LX1

3lx1


Resolution: 2.802→29.962 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 1544 5.03 %random
Rwork0.2006 ---
obs0.2035 30681 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.802→29.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 90 0 4598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014644
X-RAY DIFFRACTIONf_angle_d1.366252
X-RAY DIFFRACTIONf_dihedral_angle_d17.3141780
X-RAY DIFFRACTIONf_chiral_restr0.051704
X-RAY DIFFRACTIONf_plane_restr0.006794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8023-2.89270.35941300.30022317X-RAY DIFFRACTION88
2.8927-2.9960.31971200.28712612X-RAY DIFFRACTION98
2.996-3.11580.33171470.27482637X-RAY DIFFRACTION100
3.1158-3.25740.30741380.23552697X-RAY DIFFRACTION100
3.2574-3.42890.30521330.23582660X-RAY DIFFRACTION100
3.4289-3.64340.32441480.22682634X-RAY DIFFRACTION100
3.6434-3.92420.26451310.20442688X-RAY DIFFRACTION100
3.9242-4.3180.22121470.19772689X-RAY DIFFRACTION100
4.318-4.94050.21691620.1642660X-RAY DIFFRACTION100
4.9405-6.21530.26961520.19842716X-RAY DIFFRACTION100
6.2153-29.96410.24131360.17512827X-RAY DIFFRACTION100

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