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- PDB-7r31: 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: 7r31 | ||||||
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Title | Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803, C105A+C110A variant, in complex with ATP (co-crystal), tetragonal crystal form | ||||||
![]() | Membrane-associated protein slr1513 | ||||||
![]() | 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'-TRIPHOSPHATE / Membrane-associated protein slr1513![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Selim, K.A. / Albrecht, R. / Hartmann, M.D. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r2yC ![]() 7r2zC ![]() 7r30C ![]() 7r32C ![]() 5o3pS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 13157.979 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 244 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES PH 6.5, 25 % (W/V) PEG1000 |
-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: Feb 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→33.85 Å / Num. obs: 71568 / % possible obs: 98.8 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.52→1.61 Å / Redundancy: 8.11 % / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 11257 / CC1/2: 0.932 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5O3P Resolution: 1.52→33.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.22 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.064 / 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: 78.14 Å2 / Biso mean: 28.089 Å2 / Biso min: 14.73 Å2
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Refinement step | Cycle: final / Resolution: 1.52→33.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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