+Open data
-Basic information
Entry | Database: PDB / ID: 6kwv | ||||||
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Title | A Crystal Structure of OspA mutant | ||||||
Components | Outer surface protein A | ||||||
Keywords | LIPID BINDING PROTEIN / Outer surface protein A / OspA | ||||||
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: 1.37 Å | ||||||
Authors | Kiya, M. / Makabe, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2024 Title: beta-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking. Authors: Kiya, M. / Shiga, S. / Ding, P. / Koide, 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 | 6kwv.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kwv.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/6kwv ftp://data.pdbj.org/pub/pdb/validation_reports/kw/6kwv | HTTPS FTP |
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-Related structure data
Related structure data | 6kwjC 6kwuC 6ljyC 7fddC 7fjrC 2g8cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25878.732 Da / Num. of mol.: 1 Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,S118N,K119G,F126S,N127S,E128N,K129G,G130S,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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 38% PEG 400, 0.1M Tris pH 8.0, 15.4mg/mL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→50 Å / Num. obs: 48779 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.37→1.42 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 8.94 / Num. unique obs: 2469 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G8C Resolution: 1.37→18.43 Å / SU ML: 0.1338 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.862
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→18.43 Å
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Refine LS restraints |
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LS refinement shell |
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