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Open data
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Basic information
Entry | Database: PDB / ID: 8jv3 | ||||||
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Title | Structure of the SAR11 PotD in complex with glycine betaine | ||||||
![]() | Spermidine/putrescine-binding periplasmic protein | ||||||
![]() | TRANSPORT PROTEIN / PotD / substrate binding protein / solute-binding protein / periplasmic binding protein / ABC transporter system receptor / osmolyte / compatible solute / betaine / DMSP / GABA / amino acid / SAR11 / Candidatus Pelagibacter sp. HTCC7211 | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / TRIMETHYL GLYCINE / Spermidine/putrescine-binding periplasmic protein![]() | ||||||
Biological species | Pelagibacter sp. | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, Q. / Liu, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the SAR11 PotD in complex with glycine betaine Authors: Ma, Q. / Liu, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.7 KB | Display | ![]() |
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PDB format | ![]() | 133.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39442.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: potD, PB7211_697 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 426 molecules ![](data/chem/img/BET.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-BET / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The protein was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, pH7.5) and 1 ul reservoir solution (100 mM MES pH 6.5, 22% w/v mPEG 550). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→55.869 Å / Num. obs: 85121 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Rsym value: 0.073 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.41→1.434 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4225 / CC1/2: 0.783 / Rpim(I) all: 0.336 / Rrim(I) all: 1.15 / Rsym value: 1.099 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→26.313 Å
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Refine LS restraints |
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LS refinement shell |
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