+Open data
-Basic information
Entry | Database: PDB / ID: 2oy7 | ||||||
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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: 1.55 Å | ||||||
Authors | Makabe, K. / Terechko, V. / Koide, A. / 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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Remark 999 | SEQUENCE THERE IS AN INSERTION BETWEEN SEQUENCE DATABASE REFERENCE RESIDUES 118 AND 119. THE ...SEQUENCE THERE IS AN INSERTION BETWEEN SEQUENCE DATABASE REFERENCE RESIDUES 118 AND 119. THE SEQUENCE OF THE INSERTION IS KSSTYEKFNEKGELSEKYITRADKSSTYEKFNEKGELSEKYITRADKSSTYEKFNE KGELSEKYITRAD |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oy7.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oy7.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 2oy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/2oy7 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/2oy7 | HTTPS FTP |
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-Related structure data
Related structure data | 2oy8C 2oybC 2hkdS 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: 34670.445 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: 2.64 Å3/Da / Density % sol: 53.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97105 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97105 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 53372 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.82 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.98 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HKD Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.006 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.083 / 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: 25.758 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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