+Open data
-Basic information
Entry | Database: PDB / ID: 8chx | |||||||||
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Title | Structure and function of LolA from Vibrio cholerae | |||||||||
Components | Outer-membrane lipoprotein carrier protein | |||||||||
Keywords | LIPID TRANSPORT / Lipid / periplasm / gram-negative | |||||||||
Function / homology | Outer membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / lipoprotein localization to outer membrane / lipoprotein transport / periplasmic space / Outer-membrane lipoprotein carrier protein Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Jaiman, D. / Nagampalli, R. / Persson, K. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Sci Rep / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8chx.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8chx.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 8chx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/8chx ftp://data.pdbj.org/pub/pdb/validation_reports/ch/8chx | HTTPS FTP |
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-Related structure data
Related structure data | 8cgmC 8cm1C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23789.393 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: lolA, VC0395_A0626, VC395_1122 / Plasmid: petHis1a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5F2G9 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MES pH 5.0, 20 mM Zinc-acetate, 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.83 Å / Num. obs: 37905 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.034 / Rrim(I) all: 0.108 / Χ2: 1.07 / Net I/σ(I): 15.3 / Num. measured all: 375785 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.711 / Num. unique obs: 2234 / CC1/2: 0.871 / Rpim(I) all: 0.234 / Rrim(I) all: 0.749 / Χ2: 0.93 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.8 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 26.8 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.8 Å
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Refine LS restraints |
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