+Open data
-Basic information
Entry | Database: PDB / ID: 5ys7 | ||||||
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Title | Crystal structure of an OspA mutant | ||||||
Components | Outer Surface Protein A | ||||||
Keywords | DE NOVO PROTEIN / outer surface protein A / OspA | ||||||
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: 2.1 Å | ||||||
Authors | Takada, S. / Makabe, K. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of an OspA mutant Authors: Takada, 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 | 5ys7.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ys7.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ys7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/5ys7 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5ys7 | HTTPS FTP |
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-Related structure data
Related structure data | 6kt1C 3ckaS 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: 34540.438 Da / Num. of mol.: 1 / Mutation: L112A, L135A, E158F, K160Y, L181F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWU8 |
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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: 2.42 Å3/Da / Density % sol: 49.15 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M Tris-HCl, 30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 20560 / % possible obs: 99.8 % / Redundancy: 10.3 % / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1032 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CKA Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.346 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.942 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→20 Å
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Refine LS restraints |
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