+Open data
-Basic information
Entry | Database: PDB / ID: 6ics | ||||||
---|---|---|---|---|---|---|---|
Title | Loop deletion mutant (deleting four residues) | ||||||
Components | Outer surface protein A | ||||||
Keywords | DE NOVO PROTEIN / Outer surface protein A / OspA / LIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Shiga, S. / Makabe, K. | ||||||
Citation | Journal: Chembiochem / Year: 2019 Title: Domain-Swapping Design by Polyproline Rod Insertion. Authors: Shiga, S. / Yamanaka, M. / Fujiwara, W. / Hirota, S. / Goda, S. / Makabe, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ics.cif.gz | 68 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ics.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ics.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/6ics ftp://data.pdbj.org/pub/pdb/validation_reports/ic/6ics | HTTPS FTP |
---|
-Related structure data
Related structure data | 6aisC 6idcC 6ieiC 6iysC 2g8cS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26079.156 Da / Num. of mol.: 1 / Mutation: deletions 206-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) 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: 2.22 Å3/Da / Density % sol: 44.63 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 40% w/v PEG 400, 0.1M Imidazole |
-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 R 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: 1.4→20 Å / Num. obs: 45139 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 2252 / % possible all: 99.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G8C Resolution: 1.4→19.686 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.08
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→19.686 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|