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- PDB-1k51: A G55A Mutation Induces 3D Domain Swapping in the B1 Domain of Pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k51 | ||||||
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Title | A G55A Mutation Induces 3D Domain Swapping in the B1 Domain of Protein L from Peptostreptococcus magnus | ||||||
![]() | Protein L | ||||||
![]() | PROTEIN BINDING / Protein L B1 domain / strained beta-hairpin turn / positive phi angles / domain swapping / amyloid formation | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | O'Neill, J.W. / Kim, D.E. / Johnsen, K. / Baker, D. / Zhang, K.Y.J. | ||||||
![]() | ![]() Title: Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Authors: O'Neill, J.W. / Kim, D.E. / Johnsen, K. / Baker, D. / Zhang, K.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.3 KB | Display | ![]() |
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PDB format | ![]() | 18.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411 KB | Display | ![]() |
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Full document | ![]() | 411 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k50C ![]() 1k52C ![]() 1k53C ![]() 1hz5S 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 on special symmetry positions |
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Details | The second half of the 3D domain swapped dimer structure is generated by: -X,Y,1/2 |
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Components
#1: Protein | Mass: 8066.934 Da / Num. of mol.: 1 / Fragment: B1 domain (Residues 111-173) / Mutation: G55A, Y47W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 225mM ZnOAc, 2% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 28, 1999 / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 10417 / Num. obs: 10272 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.061 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 2.9 / Num. unique all: 980 / Rsym value: 0.133 / % possible all: 95.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 58197 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Rmerge(I) obs: 0.134 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1hZ5 Resolution: 1.8→23.46 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1343900.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Maximum Likelihood
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.2605 Å2 / ksol: 0.36815 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→23.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 25 Å / % reflection Rfree: 4.8 % / Rfactor obs: 0.186 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.229 / Rfactor Rwork: 0.212 |