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Open data
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Basic information
Entry | Database: PDB / ID: 3ckf | ||||||
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Title | The crystal structure of OspA deletion mutant | ||||||
![]() | Outer surface protein A | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Makabe, K. / Koide, S. | ||||||
![]() | ![]() Title: The promiscuity of beta-strand pairing allows for rational design of beta-sheet face inversion Authors: Makabe, K. / Koide, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.2 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ckgC ![]() 2g8cS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 23852.650 Da / Num. of mol.: 1 Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,K216S,E217S,K231S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ospA / Plasmid: pET24a / Production host: ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
Sequence details | SEQUENCE DATABASE REFERENCE RESIDUES 116-138 WERE DELETED IN THE SEQUENCE. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.45 Details: 38% PEG400, 0.1M Imidazole, 0.05M MgSO4, 11mg/ml, pH 6.45, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.25→50 Å / Num. obs: 54134 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 5.18 / Num. unique all: 4716 / % possible all: 84.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2G8C Resolution: 1.25→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.556 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / 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: 13.489 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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