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- PDB-7tm2: Porous framework formed by assembly of a bipyridyl-conjugated hel... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tm2 | ||||||
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Title | Porous framework formed by assembly of a bipyridyl-conjugated helical peptide | ||||||
![]() | helical peptide | ||||||
![]() | DE NOVO PROTEIN / porous / framework / helix / 310 / alpha / assembly / bipyridine / UIC-1 | ||||||
Function / homology | ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77 / tert-butylbenzene![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, A.I. | ||||||
Funding support | 1items
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![]() | ![]() Title: Assembly of pi-Stacking Helical Peptides into a Porous and Multivariable Proteomimetic Framework. Authors: Heinz-Kunert, S.L. / Pandya, A. / Dang, V.T. / Tran, P.N. / Ghosh, S. / McElheny, D. / Santarsiero, B.D. / Ren, Z. / Nguyen, A.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.2 KB | Display | ![]() |
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PDB format | ![]() | 14.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.2 KB | Display | ![]() |
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Full document | ![]() | 775.1 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 3.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tlsSC ![]() 7tluC ![]() 7tm1C ![]() 7tmaC ![]() 7tmeC ![]() 7tmhC ![]() 7tmiC ![]() 7tmjC ![]() 7tmkC ![]() 7tmlC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 897.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
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#2: Chemical | ChemComp-I77 / | ||||
#3: Chemical | ChemComp-I6W / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.41 % |
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Crystal grow | Temperature: 298 K / Method: slow cooling / Details: water and acetonitrile |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.619 Å / Relative weight: 1 |
Reflection | Resolution: 0.88→12.84 Å / Num. obs: 14928 / % possible obs: 95.71 % / Redundancy: 12.4 % / Biso Wilson estimate: 4.54 Å2 / Rmerge(I) obs: 0.06869 / Net I/σ(I): 16.04 |
Reflection shell | Resolution: 0.88→0.9114 Å / Rmerge(I) obs: 0.06869 / Num. unique obs: 456 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7TLS Resolution: 0.88→12.84 Å / SU ML: 0.0751 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 12.1999 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: 5.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.88→12.84 Å
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Refine LS restraints |
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LS refinement shell |
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