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- PDB-8pay: Structure of the E.coli DNA polymerase sliding clamp with a coval... -

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Basic information

Entry
Database: PDB / ID: 8pay
TitleStructure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 2.
Components
  • ACE-GLN-ALC-GLC-LEU-PHE
  • Beta sliding clamp
KeywordsREPLICATION / sliding clamp / covalent peptide / antibiotics
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit / DNA polymerase III, beta sliding clamp / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / :
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsCompain, G. / Monsarrat, C. / Blagojevic, J. / Brillet, K. / Dumas, P. / Hammann, P. / Kuhn, L. / Martiel, I. / Engilberge, S. / Olieric, V. ...Compain, G. / Monsarrat, C. / Blagojevic, J. / Brillet, K. / Dumas, P. / Hammann, P. / Kuhn, L. / Martiel, I. / Engilberge, S. / Olieric, V. / Wolff, P. / Burnouf, D. / wagner, J. / Guichard, G.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-ASTR-0002 France
Agence Nationale de la Recherche (ANR)ANR-22-CE18-0037 France
CitationJournal: Jacs Au / Year: 2024
Title: Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp.
Authors: Compain, G. / Monsarrat, C. / Blagojevic, J. / Brillet, K. / Dumas, P. / Hammann, P. / Kuhn, L. / Martiel, I. / Engilberge, S. / Olieric, V. / Wolff, P. / Burnouf, D.Y. / Wagner, J. / Guichard, G.
History
DepositionJun 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 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: Beta sliding clamp
H: ACE-GLN-ALC-GLC-LEU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8079
Polymers41,7242
Non-polymers1,0837
Water7,386410
1
A: Beta sliding clamp
H: ACE-GLN-ALC-GLC-LEU-PHE
hetero molecules

A: Beta sliding clamp
H: ACE-GLN-ALC-GLC-LEU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,61418
Polymers83,4484
Non-polymers2,16614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8690 Å2
ΔGint-14 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.858, 66.537, 80.798
Angle α, β, γ (deg.)90.00, 128.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta sliding clamp


Mass: 41009.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaN / Production host: Escherichia coli (E. coli) / References: UniProt: C3SLM2
#2: Protein/peptide ACE-GLN-ALC-GLC-LEU-PHE


Mass: 713.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.2 M Sodium fluoride 20% PEG 3350, pH 7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→52.61 Å / Num. obs: 110085 / % possible obs: 96 % / Redundancy: 13.6 % / CC1/2: 0.99 / Net I/σ(I): 21
Reflection shellResolution: 1.21→1.31 Å / Num. unique obs: 5493 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→52.61 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 5587 5.08 %
Rwork0.1498 --
obs0.1517 110085 79.89 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.21→52.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 51 410 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011584
X-RAY DIFFRACTIONf_angle_d1.172
X-RAY DIFFRACTIONf_dihedral_angle_d16.684485
X-RAY DIFFRACTIONf_chiral_restr0.097490
X-RAY DIFFRACTIONf_plane_restr0.012577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.230.10330.333139X-RAY DIFFRACTION1
1.23-1.240.3502170.3188275X-RAY DIFFRACTION7
1.24-1.260.336260.302585X-RAY DIFFRACTION13
1.26-1.270.3474300.2831741X-RAY DIFFRACTION17
1.27-1.290.3096730.28861153X-RAY DIFFRACTION27
1.29-1.310.32471200.27241841X-RAY DIFFRACTION43
1.31-1.320.28281320.26182476X-RAY DIFFRACTION57
1.32-1.340.29411790.26132980X-RAY DIFFRACTION69
1.34-1.360.3071830.24993383X-RAY DIFFRACTION78
1.36-1.390.29212280.23323804X-RAY DIFFRACTION88
1.39-1.410.27022270.22344156X-RAY DIFFRACTION96
1.41-1.440.26792090.20244300X-RAY DIFFRACTION99
1.44-1.460.22742510.18684357X-RAY DIFFRACTION100
1.46-1.490.22542150.16664405X-RAY DIFFRACTION100
1.49-1.530.19542250.14954323X-RAY DIFFRACTION100
1.53-1.560.20832310.13524375X-RAY DIFFRACTION100
1.56-1.60.15662040.12834348X-RAY DIFFRACTION100
1.6-1.640.16182410.1284353X-RAY DIFFRACTION100
1.64-1.690.16142580.12614339X-RAY DIFFRACTION100
1.69-1.750.17762150.12464372X-RAY DIFFRACTION100
1.75-1.810.16082140.12444356X-RAY DIFFRACTION100
1.81-1.880.16712190.13174411X-RAY DIFFRACTION100
1.88-1.970.18132260.13144352X-RAY DIFFRACTION100
1.97-2.070.18072350.13944404X-RAY DIFFRACTION100
2.07-2.20.18332000.13444358X-RAY DIFFRACTION100
2.2-2.370.16292310.13914413X-RAY DIFFRACTION100
2.37-2.610.17882550.14824346X-RAY DIFFRACTION100
2.61-2.990.19852810.15084352X-RAY DIFFRACTION100
2.99-3.760.18312330.15044416X-RAY DIFFRACTION100
3.77-52.610.18422260.15464485X-RAY DIFFRACTION100

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