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Yorodumi- PDB-6fxe: BBE31 from Lyme disease agent Borrelia (Borreliella) burgdorferi ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fxe | ||||||
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Title | BBE31 from Lyme disease agent Borrelia (Borreliella) burgdorferi playing a vital role in successful colonization of the mammalian host | ||||||
Components | Putative surface protein | ||||||
Keywords | PROTEIN BINDING / Outer surface protein / borrelia outer membrane / pFam54 family / glutathione binding | ||||||
Function / homology | Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / GLUTATHIONE / Putative surface protein Function and homology information | ||||||
Biological species | Borrelia burgdorferi B31 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K. | ||||||
Funding support | Latvia, 1items
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Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2019 Title: BBE31 from the Lyme disease agent Borrelia burgdorferi, known to play an important role in successful colonization of the mammalian host, shows the ability to bind glutathione. Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Zelencova, D. / Jekabsons, A. / Jaudzems, K. / Tars, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fxe.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fxe.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 6fxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fxe_validation.pdf.gz | 1020.5 KB | Display | wwPDB validaton report |
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Full document | 6fxe_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6fxe_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 6fxe_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/6fxe ftp://data.pdbj.org/pub/pdb/validation_reports/fx/6fxe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24255.869 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: First four amino acids (GAMG) are remnants from the expression tag. Source: (gene. exp.) Borrelia burgdorferi B31 (bacteria) / Gene: BB_E31 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O50725 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.55 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M Ammonium sulfate 0.1M Sodium acetate 26% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→75.17 Å / Num. obs: 19149 / % possible obs: 96.6 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 2777 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→57.19 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.186 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.434 / ESU R Free: 0.276 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.66 Å2 / Biso mean: 45.507 Å2 / Biso min: 18.81 Å2
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Refinement step | Cycle: final / Resolution: 2.4→57.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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