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- PDB-8cgm: Structure of the lipoprotein transporter LolA from Porphyromonas ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cgm | |||||||||
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Title | Structure of the lipoprotein transporter LolA from Porphyromonas gingivalis | |||||||||
![]() | Outer membrane lipoprotein carrier protein LolA | |||||||||
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Function / homology | Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Persson, K. / Jaiman, D. / Nagampalli, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A comparative analysis of lipoprotein transport proteins: LolA and LolB from Vibrio cholerae and LolA from Porphyromonas gingivalis. Authors: Jaiman, D. / Nagampalli, R. / Persson, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.8 KB | Display | ![]() |
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PDB format | ![]() | 74.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8chxC ![]() 8cm1C 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23954.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PG_1635 / Plasmid: pETHisA / Production host: ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-GOL / | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.6 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Na formate, 0.2 M NH4acetate, 0.2 M Na citrate tribasic, 0.2 M Na/K tartrate, 0.1 M imidazole/MES pH 6.5, 40% PEG500mme, 20% PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→49.72 Å / Num. obs: 41710 / % possible obs: 100 % / Redundancy: 25.4 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.038 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.7→1.761 Å / Redundancy: 26.9 % / Rmerge(I) obs: 1.299 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4084 / CC1/2: 0.865 / Rpim(I) all: 0.359 / Rrim(I) all: 1.349 / % 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: 1.7→49.72 Å
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Refine LS restraints |
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LS refinement shell |
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