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- PDB-8s4t: DNA bound structure of PrgE from plasmid pCF10 -

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Basic information

Entry
Database: PDB / ID: 8s4t
TitleDNA bound structure of PrgE from plasmid pCF10
Components
  • DNA
  • PrgE
KeywordsDNA BINDING PROTEIN / SSB
Function / homologyTRIETHYLENE GLYCOL / DNA / DNA (> 10) / PrgE
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsBreidenstein, A. / Berntsson, R.P.-A.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
Knut and Alice Wallenberg Foundation Sweden
Carl Trygger FoundationCTS 18:39 Sweden
CitationJournal: Life Sci Alliance / Year: 2024
Title: PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.
Authors: Breidenstein, A. / Lamy, A. / Bader, C.P. / Sun, W.S. / Wanrooij, P.H. / Berntsson, R.P.
History
DepositionFeb 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PrgE
B: PrgE
C: PrgE
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2516
Polymers69,9514
Non-polymers3002
Water1629
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Upon binding DNA, the protein forms a polymeric structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint12 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.776, 90.043, 131.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein PrgE / PrgK


Mass: 17067.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria)
Gene: prgK, prgE, EGX33_13060, EU507_13905, F6H88_002583, FDO46_002730, H9Q64_07920, HRF81_13830, IHC34_002761, KCT30_002803, NAG05_14735
Production host: Escherichia coli (E. coli) / References: UniProt: D1LHE9
#2: DNA chain DNA


Mass: 18747.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.22 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15 % Polyethylene glycol 400, 50 mM MES pH 6.5, 80 mM Magnesium acetate, 15 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.67→49.74 Å / Num. obs: 26266 / % possible obs: 99.75 % / Redundancy: 6.7 % / Biso Wilson estimate: 73.16 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.1158 / Net I/σ(I): 10.71
Reflection shellResolution: 2.67→2.765 Å / Redundancy: 7 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2536 / CC1/2: 0.628 / Rrim(I) all: 2.067 / % possible all: 99.06

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→49.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 41.065 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25257 1275 4.9 %RANDOM
Rwork0.22939 24963 --
all0.231 ---
obs0.23052 24963 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--1.24 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 2.67→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 315 20 9 3716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123809
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163389
X-RAY DIFFRACTIONr_angle_refined_deg0.6831.6795163
X-RAY DIFFRACTIONr_angle_other_deg0.2541.5757856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.091515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97510660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0350.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5325.8791629
X-RAY DIFFRACTIONr_mcbond_other1.5325.881629
X-RAY DIFFRACTIONr_mcangle_it2.73110.562031
X-RAY DIFFRACTIONr_mcangle_other2.73110.5632032
X-RAY DIFFRACTIONr_scbond_it1.4055.9582180
X-RAY DIFFRACTIONr_scbond_other1.4045.9592181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.58610.8163133
X-RAY DIFFRACTIONr_long_range_B_refined5.06362.64090
X-RAY DIFFRACTIONr_long_range_B_other5.06362.614091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 96 -
Rwork0.468 1778 -
obs--98.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.09550.65680.48451.04340.49650.7293-0.0454-0.2485-0.10920.09010.0368-0.04860.028-0.09270.00860.0530.02080.01870.90110.01550.018212.356621.11473.486
22.5348-0.0601-0.34211.1020.64213.2625-0.1383-0.35930.35980.12150.05710.0913-0.1397-0.08490.08110.16640.0899-0.00880.7023-0.10570.067528.865939.920924.5688
32.7872-0.4736-0.62531.4848-0.23772.0906-0.25320.4776-0.2871-0.1990.1420.1060.2458-0.08210.11120.1064-0.04450.02780.9856-0.10730.042616.607352.883252.9814
41.3147-0.1203-0.11290.04450.02730.042-0.2173-0.69370.20650.08440.19370.02790.13230.01340.02360.4386-0.02290.13761.585-0.09730.157812.320530.640828.4824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 136
2X-RAY DIFFRACTION2B1 - 136
3X-RAY DIFFRACTION3C1 - 136
4X-RAY DIFFRACTION4D1 - 15

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