+Open data
-Basic information
Entry | Database: PDB / ID: 8p33 | ||||||
---|---|---|---|---|---|---|---|
Title | BB0238 from Borrelia burgdorferi | ||||||
Components | BB0238 | ||||||
Keywords | MEMBRANE PROTEIN / Lyme disease / borreliosis / outer surface protein / immune evasion | ||||||
Function / homology | membrane / Uncharacterized protein Function and homology information | ||||||
Biological species | Borreliella burgdorferi B31 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Brangulis, K. / Foor, S.D. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Linden, S.B. / Altieri, A.S. / Akopjana, I. ...Brangulis, K. / Foor, S.D. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Linden, S.B. / Altieri, A.S. / Akopjana, I. / Baljinnyam, B. / Nelson, D.C. / Simeonov, A. / Herzberg, O. / Caimano, M.J. / Pal, U. | ||||||
Funding support | Latvia, 1items
| ||||||
Citation | Journal: Mbio / Year: 2023 Title: A unique borrelial protein facilitates microbial immune evasion. Authors: Foor, S.D. / Brangulis, K. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Alreja, A.B. / Linden, S.B. / Altieri, A.S. / Baljinnyam, B. / Akopjana, I. / Nelson, D.C. / ...Authors: Foor, S.D. / Brangulis, K. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Alreja, A.B. / Linden, S.B. / Altieri, A.S. / Baljinnyam, B. / Akopjana, I. / Nelson, D.C. / Simeonov, A. / Herzberg, O. / Caimano, M.J. / Pal, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8p33.cif.gz | 41.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8p33.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 8p33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p33_validation.pdf.gz | 426.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8p33_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 8p33_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 8p33_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/8p33 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/8p33 | HTTPS FTP |
-Related structure data
Related structure data | 8p32C 8sotC 7zxh S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16368.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: First 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage. Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0238 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51254 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.38 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M D,L-malic acid pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.97 Å / Num. obs: 9268 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.027 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 752 / CC1/2: 0.957 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZXH 7zxh Resolution: 2.1→39.31 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.342 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.9 Å2 / Biso mean: 54.201 Å2 / Biso min: 34.36 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→39.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|