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- PDB-7obj: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7obj | ||||||
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Title | Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with cyclic di-AMP (c-di-AMP) | ||||||
![]() | Membrane-associated protein slr1513 | ||||||
![]() | SIGNALING PROTEIN / SbtB / Carbon Sensing / PII-like / Cyanobacteria | ||||||
Function / homology | Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / plasma membrane-derived thylakoid membrane / Chem-2BA / Membrane-associated protein slr1513![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Selim, K.A. / Albrecht, R. / Hartmann, M.D. | ||||||
![]() | ![]() Title: Diurnal metabolic control in cyanobacteria requires perception of second messenger signaling molecule c-di-AMP by the carbon control protein SbtB. Authors: Selim, K.A. / Haffner, M. / Burkhardt, M. / Mantovani, O. / Neumann, N. / Albrecht, R. / Seifert, R. / Kruger, L. / Stulke, J. / Hartmann, M.D. / Hagemann, M. / Forchhammer, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.3 KB | Display | ![]() |
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PDB format | ![]() | 105.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o3rS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 13222.110 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M phosphate-citrate pH 4.2, 40% (w/v) PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.74 Å / Num. obs: 24685 / % possible obs: 99.7 % / Redundancy: 10.3 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.61 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 10.1 % / Rmerge(I) obs: 2.231 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 3942 / CC1/2: 0.43 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5O3R Resolution: 2→32.74 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.758 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.69 Å2 / Biso mean: 57.982 Å2 / Biso min: 35.23 Å2
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Refinement step | Cycle: final / Resolution: 2→32.74 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.049 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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