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Open data
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Basic information
Entry | Database: PDB / ID: 8ac8 | ||||||
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Title | The nucleoprotein complex of Rep protein with DUE ssDNA | ||||||
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![]() | DNA BINDING PROTEIN / Replication initiation protein Nucleoprotein complex Nucleic acid binding DNA binding | ||||||
Function / homology | ![]() plasmid maintenance / DNA replication initiation / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nowacka, M. / Wegrzyn, K. / Oliwa, M. / Konieczny, I. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268.3 KB | Display | ![]() |
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PDB format | ![]() | 177.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.9 KB | Display | ![]() |
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Full document | ![]() | 447.8 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aanC ![]() 1repS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29343.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 2719.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, ethylene glycol, HEPES, halogens |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.6→1.69 Å / Num. unique obs: 12422 / CC1/2: 0.431 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→36.85 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.205163594144 Å / Origin y: 20.4154722962 Å / Origin z: 0.528084942233 Å
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Refinement TLS group | Selection details: all |