+Open data
-Basic information
Entry | Database: PDB / ID: 8sot | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the PPIase domain of borrelial BB0108 | ||||||
Components | Basic membrane protein | ||||||
Keywords | CHAPERONE / peptidyl prolyl cis/trans isomerase / parvulin fold / PrsA / SurA | ||||||
Function / homology | SurA-like N-terminal domain / Trigger factor/SurA domain superfamily / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Peptidyl-prolyl cis-trans isomerase domain superfamily / peptidyl-prolyl cis-trans isomerase activity / Basic membrane protein Function and homology information | ||||||
Biological species | Borreliella burgdorferi B31 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Shakya, A.K. / Herzberg, O. | ||||||
Funding support | United States, 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 | 8sot.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8sot.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 8sot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sot_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8sot_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 8sot_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 8sot_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/8sot ftp://data.pdbj.org/pub/pdb/validation_reports/so/8sot | HTTPS FTP |
-Related structure data
Related structure data | 8p32C 8p33C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13110.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 6-residue amino acid Insertion at the C-ter due to a cloning artifact. N-ter insertion of L1.B31 Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Strain: ATCC 35210 / DSM 4680 / CIP 102532 / B31 / Gene: BB_0108 / Plasmid: pGEX-6-P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51135 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.86 % / Description: Rectangular plate shape |
---|---|
Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 10% 2 propanol, 0.1M Bicine, 30% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→31.47 Å / Num. obs: 13591 / % possible obs: 96.47 % / Redundancy: 3.1 % / Biso Wilson estimate: 29.71 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Rrim(I) all: 0.07 / Net I/σ(I): 13.52 |
Reflection shell | Resolution: 1.99→2.063 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.67 / Num. unique obs: 1297 / CC1/2: 0.915 / CC star: 0.978 / Rpim(I) all: 0.17 / Rrim(I) all: 0.32 / % possible all: 92.17 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→31.47 Å / SU ML: 0.2509 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.3684 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→31.47 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|