+Open data
-Basic information
Entry | Database: PDB / ID: 3aum | ||||||
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Title | Crystal structure of OspA mutant | ||||||
Components | Outer surface protein A | ||||||
Keywords | MEMBRANE PROTEIN / Beta-mender | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Makabe, K. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Aromatic cluster mutations produce focal modulations of beta-sheet structure. Authors: Biancalana, M. / Makabe, K. / Yan, S. / Koide, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aum.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aum.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 3aum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/3aum ftp://data.pdbj.org/pub/pdb/validation_reports/au/3aum | HTTPS FTP |
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-Related structure data
Related structure data | 2oy5SC 2pi3C 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: 26939.000 Da / Num. of mol.: 1 / Fragment: Residues 27-273 Mutation: E37S, E45S, K46S, K48A, K60A, K64S, K83A, E104S, K107S, S111Y, K113Y, T115Y, S121Y, E123W, K125Y, E134Y, I136Y, T138Y, 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: P0C926, 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: 2.24 Å3/Da / Density % sol: 45.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 24.4(mg/ml) protein, 17% PEG4000, 8.5% isopropanol, 15% Glycerol, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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 210 / Detector: CCD / Date: Jun 14, 2009 |
Radiation | Monochromator: Si(111) double crystal monochromator / 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: 30877 / % possible obs: 98 % / Observed criterion σ(F): 1 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OY5 Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.439 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R Free: 0.089 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.794 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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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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