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- PDB-6iys: Loop deletion and proline insertion mutant (deleting six residues... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6iys | ||||||
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Title | Loop deletion and proline insertion mutant (deleting six residues and inserted three proline residues) | ||||||
![]() | Outer surface protein A | ||||||
![]() | LIPID BINDING PROTEIN / Outer surface protein A / OspA | ||||||
Function / homology | Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / Outer surface protein A![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shiga, S. / Makabe, K. | ||||||
![]() | ![]() Title: Domain-Swapping Design by Polyproline Rod Insertion. Authors: Shiga, S. / Yamanaka, M. / Fujiwara, W. / Hirota, S. / Goda, S. / Makabe, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.6 KB | Display | ![]() |
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PDB format | ![]() | 42 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.5 KB | Display | ![]() |
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Full document | ![]() | 432.1 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6aisC ![]() 6icsC ![]() 6idcC ![]() 6ieiC ![]() 2g8cS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26154.311 Da / Num. of mol.: 1 Mutation: E37S,E45S,K46S,K48A,K60A,K65S,K83A,E104S,K107S,E196A,K239S,E240S,K254S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: ospA, BB_A15 / Production host: ![]() ![]() |
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Sequence details | Deletion mutant DSSAAT(205-210) to PPP (205-207) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 71.99 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7 / Details: 2.5 M Ammonium sulfate 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 18350 / % possible obs: 98.3 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 6.15 / Num. unique obs: 946 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G8C Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 23.641 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R: 0.814 / ESU R Free: 0.419 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.437 Å2
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Refinement step | Cycle: 1 / Resolution: 3→20 Å
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Refine LS restraints |
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