+
Open data
-
Basic information
Entry | Database: PDB / ID: 8jv4 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the SAR11 PotD in complex with DMSP | ||||||
![]() | 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 / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid / Spermidine/putrescine-binding periplasmic protein![]() | ||||||
Biological species | Pelagibacter sp. | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, Q. / Liu, C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure of the SAR11 PotD in complex with DMSP Authors: Ma, Q. / Liu, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 172.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 134.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 722.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 722.7 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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: ![]() ![]() |
---|
-Non-polymers , 5 types, 422 molecules ![](data/chem/img/DQY.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-DQY / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.69 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The protein in complex with DMSP was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 15 mM DMSP-Cl, pH 7.5) and 1 ul ...Details: The protein in complex with DMSP was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 15 mM DMSP-Cl, pH 7.5) and 1 ul reservoir solution (100 mM MES pH 6.5, 18% w/v mPEG 550). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: 1.445→55.8 Å / Num. obs: 77717 / % possible obs: 98.4 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rpim(I) all: 0.015 / Rrim(I) all: 0.054 / Rsym value: 0.052 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.445→1.47 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3260 / CC1/2: 0.8 / Rpim(I) all: 0.207 / Rrim(I) all: 0.553 / Rsym value: 0.508 / % possible all: 83.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.445→26.295 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|