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Open data
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Basic information
Entry | Database: PDB / ID: 5bvl | ||||||
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Title | Crystal structure of a de novo designed TIM-barrel | ||||||
![]() | designed TIM barrel sTIM11 | ||||||
![]() | ![]() ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Feldmeier, K. / Hocker, B. | ||||||
![]() | ![]() Title: De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Authors: Huang, P.S. / Feldmeier, K. / Parmeggiani, F. / Fernandez Velasco, D.A. / Hocker, B. / Baker, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.6 KB | Display | ![]() |
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PDB format | ![]() | 59.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 22896.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.7 % / Description: Needle |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 25% PEG 3350, 0.2M magnesium chloride hexahydrate, 0.1M bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2014 |
Radiation | Monochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.992→46.79 Å / Num. obs: 11894 / % possible obs: 98.26 % / Redundancy: 5.86 % / Biso Wilson estimate: 41.84 Å2 / Rmerge(I) obs: 0.05804 / Net I/σ(I): 15.24 |
Reflection shell | Resolution: 1.992→2.064 Å / Rmerge(I) obs: 0.6607 / Mean I/σ(I) obs: 1.79 / % possible all: 93.2 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Rosetta backbone model Resolution: 1.992→46.79 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.25 / Stereochemistry target values: ML
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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: 61.9 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.992→46.79 Å
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Refine LS restraints |
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LS refinement shell |
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