+Open data
-Basic information
Entry | Database: PDB / ID: 5z1o | ||||||
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Title | Crystal structure of an OspA mutant | ||||||
Components | Outer Surface Protein A | ||||||
Keywords | MEMBRANE 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 / Outer Surface Protein A Function and homology information | ||||||
Biological species | Borreliella burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Takada, S. / Makabe, K. | ||||||
Funding support | Japan, 1items
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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 | 5z1o.cif.gz | 142.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z1o.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/5z1o ftp://data.pdbj.org/pub/pdb/validation_reports/z1/5z1o | HTTPS FTP |
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-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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34464.344 Da / Num. of mol.: 2 / Mutation: L112A, L135F, E158A, K160Y, L181A 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 #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: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 28% PEG 400, 0.1M Tris-HCl pH 8.8 |
-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: May 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 43536 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 3.48 |
Reflection shell | Resolution: 2→2.03 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CKA Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.887 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.191 / 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: 33.661 Å2
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Refinement step | Cycle: 1 / Resolution: 2→20 Å
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Refine LS restraints |
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