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- PDB-5k5q: Structure of AspA-DNA complex: novel centromere bindng protein-ce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k5q | |||||||||
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Title | Structure of AspA-DNA complex: novel centromere bindng protein-centromere complex | |||||||||
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![]() | TRANSCRIPTION/DNA / AspA / centromere / segregation / archaea / pNOB8 / 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.1 KB | Display | ![]() |
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PDB format | ![]() | 120.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.2 KB | Display | ![]() |
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Full document | ![]() | 543.5 KB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rs7C ![]() 4rs8SC ![]() 5k5aC ![]() 5k5dC ![]() 5k5oC ![]() 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: 10596.363 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 9829.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 9846.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10% PEG 3000, 0.1 M sodium phosphate/citrate pH 6.2 |
-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 | Resolution: 2.649→48.018 Å / Num. obs: 22831 / % possible obs: 92.64 % / Redundancy: 4 % / Rsym value: 0.058 / Net I/σ(I): 8.5 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RS8 Resolution: 2.649→48.018 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 39.32
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 60.354 Å2 / ksol: 0.314 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.12 Å2 / Biso mean: 100.29 Å2 / Biso min: 34.79 Å2
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Refinement step | Cycle: final / Resolution: 2.649→48.018 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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