+Open data
-Basic information
Entry | Database: PDB / ID: 6kt1 | ||||||
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Title | Crystal structure of an OspA mutant | ||||||
Components | Outer surface protein A | ||||||
Keywords | LIPID BINDING PROTEIN / outer surface protein A / OspA / DE NOVO PROTEIN | ||||||
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: 1.43 Å | ||||||
Authors | Namioka, S. / makabe, K. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of an OspA mutant Authors: Namioka, 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 | 6kt1.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kt1.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kt1_validation.pdf.gz | 412.3 KB | Display | wwPDB validaton report |
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Full document | 6kt1_full_validation.pdf.gz | 412.2 KB | Display | |
Data in XML | 6kt1_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6kt1_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/6kt1 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/6kt1 | HTTPS FTP |
-Related structure data
Related structure data | 5ys7C 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: 25882.932 Da / Num. of mol.: 1 Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,E196A,K239S,E240S,K254S,S121V,E123F 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: 2.26 Å3/Da / Density % sol: 45.53 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl,40% PEG 400 |
-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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→41.69 Å / Num. obs: 42406 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.43→1.46 Å / Rmerge(I) obs: 0.452 / Num. unique obs: 2225 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G8C Resolution: 1.43→19.772 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.43→19.772 Å
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LS refinement shell | Resolution: 1.43→1.46 Å
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