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Open data
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Basic information
Entry | Database: PDB / ID: 6f0q | |||||||||
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Title | Crystal structure of Pizza6-AYW | |||||||||
![]() | Pizza6-AYW | |||||||||
![]() | DE NOVO PROTEIN / Artificial protein / beta propeller | |||||||||
Function / homology | TolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Noguchi, H. / De Zitter, E. / Van Meervelt, L. / Voet, A.R.D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Design of tryptophan-containing mutants of the symmetrical Pizza protein for biophysical studies. Authors: Noguchi, H. / Mylemans, B. / De Zitter, E. / Van Meervelt, L. / Tame, J.R.H. / Voet, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.8 KB | Display | ![]() |
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PDB format | ![]() | 171.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.8 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f0sC ![]() 6f0tC ![]() 3ww9S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25857.506 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28b / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.99 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M MIB (Mixtures of sodium malonate, imidazole, boric acid in the molar rations 2:3:3 buffer) or MMT (Mixtures of DL-malic acid, MES and Tris base in the molar rations 1:2:2 buffer) pH 5.0, 30% (w/v) PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→26.501 Å / Num. obs: 86627 / % possible obs: 94.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.062 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.8 / Rpim(I) all: 0.301 / % possible all: 92.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WW9 Resolution: 1.3→26.501 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.83 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→26.501 Å
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Refine LS restraints |
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LS refinement shell |
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