+Open data
-Basic information
Entry | Database: PDB / ID: 2i5v | ||||||
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Title | Crystal structure of OspA mutant | ||||||
Components | Outer surface protein A | ||||||
Keywords | DE NOVO PROTEIN / BETA-SHEET | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Makabe, K. / Terechko, V. / Koide, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: High-Resolution Structure of a Self-Assembly-Competent Form of a Hydrophobic Peptide Captured in a Soluble β-Sheet Scaffold. Authors: Makabe, K. / Biancalana, M. / Yan, S. / Tereshko, V. / Gawlak, G. / Miller-Auer, H. / Meredith, S.C. / Koide, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i5v.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i5v.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 2i5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/2i5v ftp://data.pdbj.org/pub/pdb/validation_reports/i5/2i5v | HTTPS FTP |
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-Related structure data
Related structure data | 2g8cS 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: 26485.807 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45040, UniProt: P0CL66*PLUS | ||
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#2: Chemical | #3: 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: 2.25 Å3/Da / Density % sol: 45.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% PEG400 0.1M Tris-HCl, pH 8, 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: 0.9795 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 93127 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 19.25 |
Reflection shell | Resolution: 1.1→1.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.88 / Num. unique all: 8153 / Rsym value: 0.318 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G8C Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.808 / SU ML: 0.018 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / 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: 9.823 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.128 Å / Total num. of bins used: 20
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