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Yorodumi- PDB-8eov: Precisely patterned nanofibers made from extendable protein multi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eov | ||||||
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Title | Precisely patterned nanofibers made from extendable protein multiplexes | ||||||
Components | C2HR1_4r | ||||||
Keywords | DE NOVO PROTEIN / de novo design / nanofibers | ||||||
Function / homology | PHOSPHATE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Bera, A.K. / Bethel, N.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Chem / Year: 2023 Title: Precisely patterned nanofibres made from extendable protein multiplexes. Authors: Neville P Bethel / Andrew J Borst / Fabio Parmeggiani / Matthew J Bick / T J Brunette / Hannah Nguyen / Alex Kang / Asim K Bera / Lauren Carter / Marcos C Miranda / Ryan D Kibler / Mila Lamb ...Authors: Neville P Bethel / Andrew J Borst / Fabio Parmeggiani / Matthew J Bick / T J Brunette / Hannah Nguyen / Alex Kang / Asim K Bera / Lauren Carter / Marcos C Miranda / Ryan D Kibler / Mila Lamb / Xinting Li / Banumathi Sankaran / David Baker / Abstract: Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the ...Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C to C and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eov.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eov.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 8eov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/8eov ftp://data.pdbj.org/pub/pdb/validation_reports/eo/8eov | HTTPS FTP |
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-Related structure data
Related structure data | 8eoxC 8eozC 8erwC 8g8iC 8ga9C 8gaaC 8gaqC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17614.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||||
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#2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0, 3.2 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→42.56 Å / Num. obs: 21628 / % possible obs: 99.76 % / Redundancy: 2 % / Biso Wilson estimate: 31.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0134 / Net I/σ(I): 23.39 |
Reflection shell | Resolution: 1.59→1.64 Å / Redundancy: 2 % / Rmerge(I) obs: 1.038 / Mean I/σ(I) obs: 0.68 / Num. unique obs: 2120 / CC1/2: 0.389 / % possible all: 99.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Designed model Resolution: 1.59→42.56 Å / SU ML: 0.2523 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1333 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: 46.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→42.56 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: -28.8783876116 Å / Origin y: 18.4154849582 Å / Origin z: 6.7860626823 Å
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Refinement TLS group | Selection details: all |