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Yorodumi- PDB-7r2z: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r2z | ||||||
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Title | Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with ATP and ADP resulting from long ATP soak | ||||||
Components | Membrane-associated protein slr1513 | ||||||
Keywords | SIGNALING PROTEIN / 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 / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Membrane-associated protein slr1513 Function and homology information | ||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Selim, K.A. / Albrecht, R. / Hartmann, M.D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Carbon signaling protein SbtB possesses atypical redox-regulated apyrase activity to facilitate regulation of bicarbonate transporter SbtA. Authors: Selim, K.A. / Haffner, M. / Mantovani, O. / Albrecht, R. / Zhu, H. / Hagemann, M. / Forchhammer, K. / Hartmann, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r2z.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r2z.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7r2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/7r2z ftp://data.pdbj.org/pub/pdb/validation_reports/r2/7r2z | HTTPS FTP |
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-Related structure data
Related structure data | 7r2yC 7r30C 7r31C 7r32C 5o3pS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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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.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr1513 / Production host: Escherichia coli (E. coli) / References: UniProt: P73954 #2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.71 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M SODIUM ACETATE, 0.1 M HEPES PH 7.5, 20 % (W/V) PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→31.45 Å / Num. obs: 12684 / % possible obs: 99.8 % / Redundancy: 7.23 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.4→2.54 Å / Rmerge(I) obs: 0.784 / Num. unique obs: 2032 / CC1/2: 0.863 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5O3P Resolution: 2.4→31.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 17.241 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.327 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→31.45 Å
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