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Open data
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Basic information
Entry | Database: PDB / ID: 5k5o | ||||||
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Title | Structure of AspA-26mer DNA complex | ||||||
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![]() | TRANSCRIPTION/DNA / AspA / centromere DNA / DNA segregation / pNOB8 / archaea / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Schumacher, M. | ||||||
![]() | ![]() Title: Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages. Authors: Schumacher, M.A. / Tonthat, N.K. / Lee, J. / Rodriguez-Castaneda, F.A. / Chinnam, N.B. / Kalliomaa-Sanford, A.K. / Ng, I.W. / Barge, M.T. / Shaw, P.L. / Barilla, D. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.5 KB | Display | ![]() |
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PDB format | ![]() | 85.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.4 KB | Display | ![]() |
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Full document | ![]() | 500 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rs7C ![]() 4rs8SC ![]() 5k5aC ![]() 5k5dC ![]() 5k5qC ![]() 5k5rC ![]() 5k5zC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11425.244 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 7987.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 7987.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.32 Å3/Da / Density % sol: 71.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1 M citrate, 0.1 M cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.18 |
Reflection | Resolution: 3.2→50.005 Å / Num. obs: 14191 / % possible obs: 84.58 % / Redundancy: 2 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.2→3.32 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RS8 Resolution: 3.2→50.005 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.42 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.939 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.2→50.005 Å
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Refine LS restraints |
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LS refinement shell |
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