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- PDB-5o3s: 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: 5o3s | ||||||
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Title | Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in Apo state, hexagonal crystal form | ||||||
![]() | Membrane-associated protein slr1513 | ||||||
![]() | SIGNALING PROTEIN / SbtB / Carbon sensing / PII-like / cyanobacteria | ||||||
Function / homology | Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / plasma membrane-derived thylakoid membrane / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Membrane-associated protein slr1513![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Selim, K.A. / Albrecht, R. / Forchhammer, K. / Hartmann, M.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: PII-like signaling protein SbtB links cAMP sensing with cyanobacterial inorganic carbon response. Authors: Selim, K.A. / Haase, F. / 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 | ![]() | 51.9 KB | Display | ![]() |
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PDB format | ![]() | 35.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.3 KB | Display | ![]() |
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Full document | ![]() | 420.3 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o3pSC ![]() 5o3qC ![]() 5o3rC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13222.110 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: PCC 6803 / Kazusa / Gene: slr1513 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.69 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 8.5 Details: Protein solution containing 19 mg/ml SbtB in 50 mM Tris.HCl (pH 8.0), 250 mM NaCl mixed 1:1 with reservoir solution composed of 0.2 M Mg chloride, 0.1 M Tris.HCl pH 8.5, and 30% (w/v) PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→36.29 Å / Num. obs: 4838 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.25 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 776 / CC1/2: 0.934 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5O3P Resolution: 2.2→36.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 38.876 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.915 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→36.29 Å
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Refine LS restraints |
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