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- PDB-4nwq: Computationally Designed Two-Component Self-Assembling Tetrahedra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nwq | ||||||
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Title | Computationally Designed Two-Component Self-Assembling Tetrahedral Cage, T33-21, Crystallized in Space Group F4132 | ||||||
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![]() | PROTEIN BINDING / two-component / self-assembling / tetrahedron / designed protein cage / computational design / protein engineering / multimerization / nanomaterial / nanostructure / transferase / isomerase | ||||||
Function / homology | ![]() 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity / corrinoid adenosyltransferase activity / : / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | McNamara, D.E. / King, N.P. / Bale, J.B. / Sheffler, W. / Baker, D. / Yeates, T.O. | ||||||
![]() | ![]() Title: Accurate design of co-assembling multi-component protein nanomaterials. Authors: King, N.P. / Bale, J.B. / Sheffler, W. / McNamara, D.E. / Gonen, S. / Gonen, T. / Yeates, T.O. / Baker, D. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
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PDB format | ![]() | 96.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.9 KB | Display | ![]() |
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Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nwnC ![]() 4nwoC ![]() 4nwpC ![]() 4nwrC ![]() 1wy1S ![]() 3e6qS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a protein cage with tetrahedral point group symmetry. One asymmetric unit contains one heterodimer, with each chain from a different homotrimer in the biological assembly. |
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Components
#1: Protein | Mass: 19316.582 Da / Num. of mol.: 1 Mutation: K85A, E88L, G89K, S92L, E95M, E126L, A130L, L133T, K140A, L143A, V144A, N147L, R148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 14346.274 Da / Num. of mol.: 1 / Mutation: A27K, A74I, Q78T, A79L, E82A, E86A, G90E, A112L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / pH: 5.5 Details: 100 mM bis-tris pH 5.5, 2.12 M (NH4)2 SO4, vapor diffusion, hanging drop, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9716 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→96.23 Å / Num. obs: 21830 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 19.77 % / Biso Wilson estimate: 68.99 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 20.91 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 20.03 % / Rmerge(I) obs: 1.277 / Mean I/σ(I) obs: 2.94 / % possible all: 99.9 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WY1 AND 3E6Q Resolution: 2.8→96.23 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 20.64 / 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: 73.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→96.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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