+Open data
-Basic information
Entry | Database: PDB / ID: 6j6b | ||||||
---|---|---|---|---|---|---|---|
Title | Borrelia burgdorferi OspA via surface entropy reduction (form2) | ||||||
Components | Outer surface protein A | ||||||
Keywords | LIPID BINDING PROTEIN / single-layer beta-sheet | ||||||
Function / homology | Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / Outer surface protein A Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Fujiwara, H. / Makabe, K. | ||||||
Citation | Journal: J Mol Liq / Year: 2019 Title: Beta-sheet elasticity of peptide self-assembly mimic, PSAM, with a grafted sequence characterized by comprehensive analyses of isomorphous crystals Authors: Fujiwara, H. / Hongo, K. / Hori, Y. / Yoshida, N. / Makabe, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6j6b.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6j6b.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 6j6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j6b_validation.pdf.gz | 418.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6j6b_full_validation.pdf.gz | 419.9 KB | Display | |
Data in XML | 6j6b_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 6j6b_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/6j6b ftp://data.pdbj.org/pub/pdb/validation_reports/j6/6j6b | HTTPS FTP |
-Related structure data
Related structure data | 5b2aC 6j5mC 6j5nC 6j5oC 6j5pC 6j5qC 6j5rC 6j6cC 6j6dC 6j6eC 2g8cS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26395.469 Da / Num. of mol.: 1 Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,E196A,K239S,E240S,K254S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria) Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: ospA, BB_A15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CL66 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Imidazole pH 7.0, 40% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 16552 / % possible obs: 91.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 815 / % possible all: 88.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G8C Resolution: 1.901→19.787 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 25.83
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→19.787 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|