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- PDB-8ac8: The nucleoprotein complex of Rep protein with DUE ssDNA -

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Basic information

Entry
Database: PDB / ID: 8ac8
TitleThe nucleoprotein complex of Rep protein with DUE ssDNA
Components
  • DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')
  • Replication initiation protein
KeywordsDNA BINDING PROTEIN / Replication initiation protein Nucleoprotein complex Nucleic acid binding DNA binding
Function / homology
Function and homology information


plasmid maintenance / DNA replication initiation / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Initiator Rep protein / Initiator Replication protein, WH1 / Initiator Rep protein, WH2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / Replication initiation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNowacka, M. / Wegrzyn, K. / Oliwa, M. / Konieczny, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/D/NZ1/00239 Poland
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation.
Authors: Wegrzyn, K. / Oliwa, M. / Nowacka, M. / Zabrocka, E. / Bury, K. / Purzycki, P. / Czaplewska, P. / Pipka, J. / Giraldo, R. / Konieczny, I.
History
DepositionJul 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Replication initiation protein
A: Replication initiation protein
B: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')
D: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)64,1274
Polymers64,1274
Non-polymers00
Water5,891327
1
C: Replication initiation protein
D: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,0632
Polymers32,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area11360 Å2
2
A: Replication initiation protein
B: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,0632
Polymers32,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-12 kcal/mol
Surface area11150 Å2
Unit cell
Length a, b, c (Å)47.400, 85.310, 146.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-372-

HOH

31A-416-

HOH

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Components

#1: Protein Replication initiation protein / Protein E / Protein rep / Protein F4


Mass: 29343.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: repE, E, rep, ECOK12F045 / Production host: Escherichia coli (E. coli) / References: UniProt: P03856
#2: DNA chain DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')


Mass: 2719.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, ethylene glycol, HEPES, halogens

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.6→36.85 Å / Num. obs: 79263 / % possible obs: 99.6 % / Redundancy: 12.99 % / Biso Wilson estimate: 33.07 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.92
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 12422 / CC1/2: 0.431

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1REP

1rep


Resolution: 1.6→36.85 Å / SU ML: 0.2999 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.0221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 1988 2.53 %
Rwork0.2121 76610 -
obs0.2129 78598 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 334 0 327 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624124
X-RAY DIFFRACTIONf_angle_d0.82775673
X-RAY DIFFRACTIONf_chiral_restr0.0535614
X-RAY DIFFRACTIONf_plane_restr0.0056668
X-RAY DIFFRACTIONf_dihedral_angle_d28.5514701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.45461270.43024954X-RAY DIFFRACTION90.47
1.64-1.680.41321380.38975385X-RAY DIFFRACTION99.44
1.68-1.730.40841420.36385418X-RAY DIFFRACTION99.8
1.73-1.790.35081410.32645441X-RAY DIFFRACTION99.84
1.79-1.850.33231420.28565469X-RAY DIFFRACTION99.82
1.85-1.930.27641420.26165441X-RAY DIFFRACTION99.91
1.93-2.020.28491420.25415471X-RAY DIFFRACTION99.95
2.02-2.120.29761420.23255494X-RAY DIFFRACTION99.95
2.12-2.260.25821430.21565495X-RAY DIFFRACTION99.95
2.26-2.430.24941420.21745485X-RAY DIFFRACTION99.98
2.43-2.670.26641440.20965538X-RAY DIFFRACTION100
2.67-3.060.24951450.21025570X-RAY DIFFRACTION99.97
3.06-3.860.20361450.18975608X-RAY DIFFRACTION99.98
3.86-36.850.21561530.18665841X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: 0.205163594144 Å / Origin y: 20.4154722962 Å / Origin z: 0.528084942233 Å
111213212223313233
T0.201574691192 Å20.0308094389933 Å20.00220673330571 Å2-0.253834502072 Å20.0144120630881 Å2--0.280592038859 Å2
L0.0419424365568 °20.148673909001 °2-0.0171372250593 °2-0.861282933284 °20.456651789469 °2--0.848853726453 °2
S-0.0219043013923 Å °-0.00522704928218 Å °-0.0355938720481 Å °0.00101681858836 Å °0.00928853962632 Å °-0.00698439814453 Å °-0.0496834719511 Å °-0.0524172779613 Å °0.0144511642011 Å °
Refinement TLS groupSelection details: all

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