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- PDB-6idc: 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: 6idc | ||||||
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Title | Loop deletion and proline insertion mutant (deleting six residues and inserted six proline residues) | ||||||
![]() | Outer surface protein A | ||||||
![]() | DE NOVO PROTEIN / Outer surface protein A / LIPID BINDING PROTEIN | ||||||
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 | ![]() | 64.7 KB | Display | ![]() |
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PDB format | ![]() | 45.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.9 KB | Display | ![]() |
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Full document | ![]() | 423 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6aisC ![]() 6icsC ![]() 6ieiC ![]() 6iysC ![]() 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: 26445.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ospA, BB_A15 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.51 Å3/Da / Density % sol: 77.69 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / 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 PILATUS3 S 6M / Detector: PIXEL / Date: Feb 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 75395 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 3794 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G8C Resolution: 2.007→19.903 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.55 / Stereochemistry target values: ML Details: The authors scaled the sample data as P3, but refined the data as P321.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.007→19.903 Å
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Refine LS restraints |
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LS refinement shell |
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