+Open data
-Basic information
Entry | Database: PDB / ID: 6kk9 | ||||||
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Title | A Crystal structure of OspA mutant | ||||||
Components | Outer Surface Protein A | ||||||
Keywords | LIPID BINDING PROTEIN / Outer surface protein A | ||||||
Function / homology | Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Outer Surface Protein A Function and homology information | ||||||
Biological species | Borreliella burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shiga, S. / Makabe, K. | ||||||
Citation | Journal: Proteins / Year: 2021 Title: Structural analysis of the beta-sheet edge of peptide self-assembly using a model protein. Authors: Shiga, S. / Makabe, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kk9.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kk9.ent.gz | 123.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kk9_validation.pdf.gz | 465.4 KB | Display | wwPDB validaton report |
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Full document | 6kk9_full_validation.pdf.gz | 474.4 KB | Display | |
Data in XML | 6kk9_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 6kk9_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/6kk9 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/6kk9 | HTTPS FTP |
-Related structure data
Related structure data | 3ckaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 21868.238 Da / Num. of mol.: 4 Mutation: L103K, L112E, L126K, L135E, L149K, K160Y, L172K, L179V, L181E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0VWU8 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 30% PEG 400, 0.1 M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 43410 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 33.1046479172 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.44 / Num. unique obs: 4307 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CKA Resolution: 2.2→19.9 Å / SU ML: 0.322766174378 / Cross valid method: FREE R-VALUE / σ(F): 1.33792902289 / Phase error: 31.6423084022
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.1874099348 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.9 Å
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Refine LS restraints |
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LS refinement shell |
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