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Yorodumi- PDB-8t5t: Crystal structure of outer membrane lipoprotein carrier protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t5t | |||||||||
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Title | Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Borrelia burgdorferi (steric acid bound) | |||||||||
Components | Outer membrane lipoprotein carrier protein (LolA) | |||||||||
Keywords | LIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Borrelia / LolA / lipoprotein carrier | |||||||||
Function / homology | Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / STEARIC ACID / Export chaperone Function and homology information | |||||||||
Biological species | Borreliella burgdorferi B31 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Borrelia burgdorferi (steric acid bound) Authors: Lovell, S. / Cooper, A. / Battaile, K.P. / Zueckert, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t5t.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t5t.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 8t5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t5t_validation.pdf.gz | 746.2 KB | Display | wwPDB validaton report |
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Full document | 8t5t_full_validation.pdf.gz | 747 KB | Display | |
Data in XML | 8t5t_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 8t5t_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/8t5t ftp://data.pdbj.org/pub/pdb/validation_reports/t5/8t5t | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23403.543 Da / Num. of mol.: 1 / Fragment: Q18-N216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_0346 / Plasmid: BobuA.17454.a.DH3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O51321 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-STE / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley E4: 1500 mM Ammonium sulfate, 100 mM Hepes pH 7.5. BobuA.17454.a.DH3.PK00001 at 10 mg/mL. plate 13170, well E4 drop 3. Puck: PSL-1107, Cryo: 2.5M lithium sulfate, Large mass of ...Details: Berkeley E4: 1500 mM Ammonium sulfate, 100 mM Hepes pH 7.5. BobuA.17454.a.DH3.PK00001 at 10 mg/mL. plate 13170, well E4 drop 3. Puck: PSL-1107, Cryo: 2.5M lithium sulfate, Large mass of electron density in the binding pocket that appeared to be a fatty acid from the expression host. Modelled as steric acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 5, 2023 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.93 Å / Num. obs: 29577 / % possible obs: 100 % / Redundancy: 39.1 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.012 / Rrim(I) all: 0.078 / Χ2: 0.96 / Net I/σ(I): 30.1 / Num. measured all: 1157377 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 39.4 % / Rmerge(I) obs: 2.755 / Num. measured all: 67350 / Num. unique obs: 1709 / CC1/2: 0.77 / Rpim(I) all: 0.443 / Rrim(I) all: 2.791 / Χ2: 0.9 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.82 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 24.67 / Stereochemistry target values: ML
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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: 1.8→28.82 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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