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- PDB-7tm1: 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: 7tm1 | ||||||
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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 | ACETONITRILE / ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, A.I. | ||||||
Funding support | ![]()
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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 | ![]() | 41.5 KB | Display | ![]() |
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PDB format | ![]() | 28.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7tlsC ![]() 7tluC ![]() 7tm2C ![]() 7tmaC ![]() 7tmeC ![]() 7tmhC ![]() 7tmiC ![]() 7tmjC ![]() 7tmkC ![]() 7tmlC 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 957.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CCN / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.73 % |
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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: Jun 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→26.62 Å / Num. obs: 17817 / % possible obs: 95.64 % / Redundancy: 3.9 % / Biso Wilson estimate: 6.94 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.228 / Net I/σ(I): 9.55 |
Reflection shell | Resolution: 1.1→1.139 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 849 / CC1/2: 0.792 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: energy minimized helix Resolution: 1.1→26.62 Å / SU ML: 0.0898 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.177 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: 9.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→26.62 Å
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Refine LS restraints |
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LS refinement shell |
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