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Open data
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Basic information
Entry | Database: PDB / ID: 8amv | |||||||||||||||||||||||||||
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Title | RepB pMV158 hexamer | |||||||||||||||||||||||||||
![]() | Replication protein RepB | |||||||||||||||||||||||||||
![]() | REPLICATION / rolling circle replication / RepB / pMV158 | |||||||||||||||||||||||||||
Function / homology | ![]() DNA topoisomerase activity / extrachromosomal circular DNA / DNA replication / DNA binding / identical protein binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Machon, C. / Amodio, J. / Boer, R.D. / Ruiz-Maso, J.A. / del Solar, G. / Coll, M. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of pMV158 replication initiator RepB with and without DNA reveal a flexible dual-function protein. Authors: Machon, C. / Ruiz-Maso, J.A. / Amodio, J. / Boer, D.R. / Bordanaba-Ruiseco, L. / Bury, K. / Konieczny, I. / Del Solar, G. / Coll, M. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 297.2 KB | Display | ![]() |
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PDB format | ![]() | 197.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.8 KB | Display | ![]() |
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Full document | ![]() | 528.4 KB | Display | |
Data in XML | ![]() | 44.8 KB | Display | |
Data in CIF | ![]() | 60.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8amtC ![]() 8amuC ![]() 3dkxS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 4 - 203 / Label seq-ID: 4 - 203
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Components
#1: Protein | Mass: 24287.105 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 100 mM Na/K phosphate pH 6.2 200 mM NaCl 10 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→45.52 Å / Num. obs: 40217 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 76.65 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.77→45.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.097 / Num. unique obs: 3702 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DKX Resolution: 2.77→45.48 Å / SU ML: 0.4368 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.332 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: 87.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.77→45.48 Å
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Refine LS restraints |
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LS refinement shell |
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