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- PDB-7osu: sTIM11noCys-SB, a de novo designed TIM barrel with a salt-bridge ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7osu | |||||||||
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Title | sTIM11noCys-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1) | |||||||||
![]() | sTIM11noCys-SB | |||||||||
![]() | DE NOVO PROTEIN / TIM barrel / salt bridge cluster | |||||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Romero-Romero, S. / Kordes, S. / Hocker, B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels. Authors: Kordes, S. / Romero-Romero, S. / Lutz, L. / Hocker, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.1 KB | Display | ![]() |
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Full document | ![]() | 435 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7osvC ![]() 7ot7C ![]() 7ot8C ![]() 7p12C ![]() 5bvlS 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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Components
#1: Protein | Mass: 22977.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: M (N-terminal) and GLEHHHHHH (C-terminal) come from the expresion vector Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b(+) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.4 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 50% PEG 200, 0.2 M NaCl, 0.1 M Phosphate citrate pH5.0 |
-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: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9874 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→47.3 Å / Num. obs: 36942 / % possible obs: 99.92 % / Redundancy: 14.1 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.024 / Rrim(I) all: 0.0904 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.37→1.42 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.04 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3614 / CC1/2: 0.66 / CC star: 0.884 / Rpim(I) all: 0.558 / Rrim(I) all: 2.11 / % possible all: 99.92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5bvl Resolution: 1.37→47.3 Å / SU ML: 0.1837 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1336 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: 36.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→47.3 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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