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Yorodumi- PDB-7a8s: de novo designed ba8-barrel sTIM11 with an alpha-helical extension -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a8s | ||||||
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Title | de novo designed ba8-barrel sTIM11 with an alpha-helical extension | ||||||
Components | sTIM11_h3 | ||||||
Keywords | DE NOVO PROTEIN / Protein design / TIM-barrel / sTIM11 | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Shanmugaratnam, S. / Wiese, J.G. / Hocker, B. | ||||||
Citation | Journal: Protein Sci. / Year: 2021 Title: Extension of a de novo TIM barrel with a rationally designed secondary structure element. Authors: Wiese, J.G. / Shanmugaratnam, S. / Hocker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a8s.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a8s.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 7a8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a8s_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 7a8s_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 7a8s_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 7a8s_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/7a8s ftp://data.pdbj.org/pub/pdb/validation_reports/a8/7a8s | HTTPS FTP |
-Related structure data
Related structure data | 5bvlS S: Starting model for refinement |
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Similar structure data |
-Links
-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: 23526.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: sTIM11_h3 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 11, 2016 / Details: vertically collimating mirror |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry, and a toroidal mirror (M2) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→47.23 Å / Num. obs: 197971 / % possible obs: 96.91 % / Redundancy: 8.1 % / Biso Wilson estimate: 25.44 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.029 / Rrim(I) all: 0.086 / Net I/σ(I): 12.75 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 2.161 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 8063 / CC1/2: 0.321 / CC star: 0.697 / Rpim(I) all: 1.178 / Rrim(I) all: 2.484 / % possible all: 78.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BVL Resolution: 1.58→47.23 Å / SU ML: 0.3038 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.905 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: 41.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→47.23 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: -15.9774998632 Å / Origin y: 8.1106254945 Å / Origin z: 6.12174854739 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 1 through 190) |