+Open data
-Basic information
Entry | Database: PDB / ID: 5b2a | ||||||
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Title | Crystal structure of a mutant of OspA | ||||||
Components | Outer surface protein A | ||||||
Keywords | MEMBRANE PROTEIN / beta-sheet / amyloid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Hori , Y. / Makabe, K. | ||||||
Citation | Journal: J Mol Liq / Year: 2019 Title: Beta-sheet elasticity of peptide self-assembly mimic, PSAM, with a grafted sequence characterized by comprehensive analyses of isomorphous crystals Authors: Fujiwara, H. / Hongo, K. / Hori, Y. / Yoshida, N. / Makabe, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b2a.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b2a.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b2a_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 5b2a_full_validation.pdf.gz | 424.2 KB | Display | |
Data in XML | 5b2a_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5b2a_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/5b2a ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b2a | HTTPS FTP |
-Related structure data
Related structure data | 6j5mC 6j5nC 6j5oC 6j5pC 6j5qC 6j5rC 6j6bC 6j6cC 6j6dC 6j6eC 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: 26345.543 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-273 Mutation: E37S,E45S,K48A,K64S,K83A,E104S,K107S,S120V,S121L,T122G,E123D,E196A,K239S,E240S,K254S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Gene: ospA / Production host: Escherichia coli (E. coli) / References: UniProt: Q45040, UniProt: P0CL66*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 40% PEG 400, 0.1M Tris pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Nov 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 27889 / % possible obs: 97.18 % / Redundancy: 3.6 % / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.6→1.63 Å |
-Processing
Software |
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Refinement | Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.515 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.359 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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