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Yorodumi- PDB-5o3s: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -
+Open data
-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 | ||||||
Components | Membrane-associated protein slr1513 | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Selim, K.A. / Albrecht, R. / Forchhammer, K. / Hartmann, M.D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o3s.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o3s.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 5o3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/5o3s ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o3s | HTTPS FTP |
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-Related structure data
Related structure data | 5o3pSC 5o3qC 5o3rC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / Gene: slr1513 / Production host: Escherichia coli (E. coli) / References: UniProt: P73954 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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