+Open data
-Basic information
Entry | Database: PDB / ID: 2oyb | ||||||
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Title | The crystal structure of OspA mutant | ||||||
Components | Outer surface protein A | ||||||
Keywords | MEMBRANE PROTEIN / beta-sheet | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Makabe, K. / Biancalana, M. / Terechko, V. / Koide, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics Authors: Biancalana, M. / Makabe, K. / Koide, A. / Koide, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oyb.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oyb.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oyb_validation.pdf.gz | 419.7 KB | Display | wwPDB validaton report |
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Full document | 2oyb_full_validation.pdf.gz | 421.7 KB | Display | |
Data in XML | 2oyb_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2oyb_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/2oyb ftp://data.pdbj.org/pub/pdb/validation_reports/oy/2oyb | HTTPS FTP |
-Related structure data
Related structure data | 2oy7C 2oy8C 2g8cS C: citing same article (ref.) 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: 26571.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Gene: ospA / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45040, UniProt: P0CL66*PLUS |
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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: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 37% PEG400, 0.1M Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 57675 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.01 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.36 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2G8C Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.447 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.053 / ESU R Free: 0.051 / 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: 11.737 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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