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Yorodumi- PDB-7tmk: Porous framework formed by assembly of a bipyridyl-conjugated hel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tmk | ||||||
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Title | Porous framework formed by assembly of a bipyridyl-conjugated helical peptide | ||||||
Components | helical peptide | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.83 Å | ||||||
Authors | Nguyen, A.I. | ||||||
Funding support | 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tmk.cif.gz | 33.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tmk.ent.gz | 22.6 KB | Display | PDB format |
PDBx/mmJSON format | 7tmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/7tmk ftp://data.pdbj.org/pub/pdb/validation_reports/tm/7tmk | HTTPS FTP |
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-Related structure data
Related structure data | 7tlsSC 7tluC 7tm1C 7tm2C 7tmaC 7tmeC 7tmhC 7tmiC 7tmjC 7tmlC S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 943.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.76 % |
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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: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 0.711 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jul 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.711 Å / Relative weight: 1 |
Reflection | Resolution: 0.83→8.88 Å / Num. obs: 18180 / % possible obs: 98.94 % / Redundancy: 6.8 % / Biso Wilson estimate: 3.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.03 |
Reflection shell | Resolution: 0.83→0.859 Å / Num. unique obs: 9944 / CC1/2: 0.886 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7TLS Resolution: 0.83→8.88 Å / SU ML: 0.0752 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.2098 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: 5.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.83→8.88 Å
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Refine LS restraints |
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LS refinement shell |
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