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Open data
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Basic information
Entry | Database: PDB / ID: 7fdd | ||||||
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Title | A Crystal structure of OspA mutant | ||||||
![]() | Outer surface protein A | ||||||
![]() | LIPOPROTEIN / 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 / DI(HYDROXYETHYL)ETHER / Outer surface protein A![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shiga, S. / Makabe, K. | ||||||
![]() | ![]() Title: beta-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking. Authors: Kiya, M. / Shiga, S. / Ding, P. / Koide, 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 | ![]() | 216.2 KB | Display | ![]() |
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PDB format | ![]() | 144.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.8 KB | Display | ![]() |
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Full document | ![]() | 467.4 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kwjC ![]() 6kwuC ![]() 6kwvC ![]() 6ljySC ![]() 7fjrC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25605.525 Da / Num. of mol.: 2 Mutation: E37S, E45S, K46S, K48A, K60A, K64S, K83A, E104S, K107S, Deletion 117-119, insertion GG, Deletion 124-127, Deletion 130-133, insertion TTT, K239S, E240S, K254S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: OspA, BB_A15 / Production host: ![]() ![]() #2: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.76 Å3/Da / Density % sol: 74.15 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: Protein (16.0 mg/mL) 36% Polyethylene glycol 400, 0.1 M Imidazole (pH7.0) |
-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: May 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19.49 Å / Num. obs: 19789 / % possible obs: 93.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 64.66 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5091 / % possible all: 84.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LJY Resolution: 2.9→19.49 Å / SU ML: 0.5099 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 34.727 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 21.3249549898 Å / Origin y: 15.9062406374 Å / Origin z: 17.4095804677 Å
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Refinement TLS group | Selection details: all |