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- PDB-8t5j: Crystal structure of outer membrane lipoprotein carrier protein (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t5j | ||||||
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Title | Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia | ||||||
![]() | Outer membrane lipocarrier LolA family protein | ||||||
![]() | LIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / lipoprotein carrier / LolA | ||||||
Function / homology | Outer membrane lipoprotein carrier protein LolA-like / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / protein transport / metal ion binding / HEXANE-1,6-DIOL / Outer membrane lipocarrier LolA family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella philomiragia Authors: Woodward, E.L. / Lovell, S. / Cooper, A. / Buchko, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 63.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 447.4 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22194.951 Da / Num. of mol.: 1 / Fragment: L32-N205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 160 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % / Description: hexagonal prisms |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley D10: 20% (w/v) PEG 3350, 100 mM Hepes pH 7.5, 100 mM Lithium sulfate, 100 mM Magnesium chloride, 10% (w/v) 1,6-Hexanediol. FrphA.20731.a.VL2.PB00125 at 14.5 mg/mL. plate 13468 well ...Details: Berkeley D10: 20% (w/v) PEG 3350, 100 mM Hepes pH 7.5, 100 mM Lithium sulfate, 100 mM Magnesium chloride, 10% (w/v) 1,6-Hexanediol. FrphA.20731.a.VL2.PB00125 at 14.5 mg/mL. plate 13468 well D10 drop1, Cryo: 80% crystallant+20% PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Jun 8, 2023 |
Radiation | Monochromator: HELIOS MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25.17 Å / Num. obs: 28420 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.02 / Rrim(I) all: 0.099 / Χ2: 0.94 / Net I/σ(I): 24.7 / Num. measured all: 718556 |
Reflection shell | Resolution: 1.55→1.58 Å / % possible obs: 100 % / Redundancy: 17 % / Rmerge(I) obs: 2.648 / Num. measured all: 23447 / Num. unique obs: 1382 / CC1/2: 0.516 / Rpim(I) all: 0.662 / Rrim(I) all: 2.73 / Χ2: 1.35 / Net I/σ(I) obs: 1.6 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→21.1 Å
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Refine LS restraints |
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LS refinement shell |
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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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