[English] 日本語
Yorodumi- PDB-6fze: BBE31 from Lyme disease agent Borrelia (Borreliella) burgdorferi ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fze | ||||||
---|---|---|---|---|---|---|---|
Title | BBE31 from Lyme disease agent Borrelia (Borreliella) burgdorferi playing a vital role in successful colonization of the mammalian host (native data) | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K. | ||||||
Funding support | Latvia, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fze.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fze.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fze_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6fze_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6fze_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 6fze_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/6fze ftp://data.pdbj.org/pub/pdb/validation_reports/fz/6fze | HTTPS FTP |
-Related structure data
Related structure data | 6fxeSC 6fzzC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.21 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2 M Ammonium sulfate 0.1 M Sodium acetate 24% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→57.95 Å / Num. obs: 23985 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.26→2.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3442 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FXE Resolution: 2.26→57.95 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.551 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.241 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.34 Å2 / Biso mean: 38.385 Å2 / Biso min: 18.83 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.26→57.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.263→2.322 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|