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- PDB-8aan: The nucleoprotein complex of Rep protein with iteron containing d... -

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Basic information

Entry
Database: PDB / ID: 8aan
TitleThe nucleoprotein complex of Rep protein with iteron containing dsDNA and DUE ssDNA.
Components
  • DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*T)-3')
  • DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)-3')
  • DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*T)-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 / DNA (> 10) / Replication initiation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsNowacka, M. / Wegrzyn, K.
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 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 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
B: DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)-3')
C: DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*T)-3')
A: Replication initiation protein
D: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2695
Polymers45,2454
Non-polymers241
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-42 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.313, 81.047, 75.833
Angle α, β, γ (deg.)90.000, 123.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

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Components

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DNA chain , 3 types, 3 molecules BCD

#1: DNA chain DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)-3')


Mass: 6687.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*T)-3')


Mass: 6807.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*T)-3')


Mass: 2406.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

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


Mass: 29343.527 Da / Num. of mol.: 1
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

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Non-polymers , 2 types, 304 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.09 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 20 000, 20% v/v PEG MME 550 0.02M of each carboxylic acid (0.2 M sodium formate, 0.2M ammonium acetate, 0.2M trisodium citrate, 0.2M sodium potassium L-tartrate, 0.2M sodium ...Details: 10% w/v PEG 20 000, 20% v/v PEG MME 550 0.02M of each carboxylic acid (0.2 M sodium formate, 0.2M ammonium acetate, 0.2M trisodium citrate, 0.2M sodium potassium L-tartrate, 0.2M sodium oxamate), 0.1M MES/imidazole pH 6.5.

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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: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.1889→29.94 Å / Num. obs: 27949 / % possible obs: 97.6 % / Redundancy: 6.615 % / CC1/2: 0.995 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1889→2.2671 Å / Num. unique obs: 4267 / CC1/2: 0.991

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1REP

1rep


Resolution: 2.19→29.94 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 1393 4.99 %
Rwork0.1865 26501 -
obs0.1887 27894 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.11 Å2 / Biso mean: 37.2766 Å2 / Biso min: 17.63 Å2
Refinement stepCycle: final / Resolution: 2.19→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 1022 0 303 3213
Biso mean---41.31 -
Num. residues----280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.270.34091310.32032484261592
2.27-2.360.39331340.31172557269196
2.36-2.470.28461390.23432652279198
2.47-2.590.29651410.226226762817100
2.59-2.760.28111410.22112663280499
2.76-2.970.28851420.21532702284499
2.97-3.270.25181400.20032680282099
3.27-3.740.22621390.16782649278898
3.74-4.710.1951440.140827322876100
4.71-29.940.16361420.15712706284898

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