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Yorodumi- PDB-8gl5: Porous framework formed by assembly of a bipyridyl-conjugated hel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gl5 | ||||||
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Title | Porous framework formed by assembly of a bipyridyl-conjugated helical peptide | ||||||
Components | LEU-AIB-ALA-SER-LEU-ALA-SNC-AIB-LEU | ||||||
Keywords | DE NOVO PROTEIN | ||||||
Function / homology | Chem-I77 / NICOTINIC ACID Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | ||||||
Authors | Hess, S.S. / Nguyen, A.I. | ||||||
Funding support | 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks. Authors: Hess, S.S. / Coppola, F. / Dang, V.T. / Tran, P.N. / Mickel, P.J. / Oktawiec, J. / Ren, Z. / Kral, P. / 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 | 8gl5.cif.gz | 19.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gl5.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gl5_validation.pdf.gz | 669.5 KB | Display | wwPDB validaton report |
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Full document | 8gl5_full_validation.pdf.gz | 670.9 KB | Display | |
Data in XML | 8gl5_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 8gl5_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/8gl5 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/8gl5 | HTTPS FTP |
-Related structure data
Related structure data | 8gb9C 8gbaC 8gbhC 8gbiC 8gbmC 8gboC 8gd6C 8gd8C 8givC 8gj7C 8gk1C 8gk2C 8gk9C 8gkbC 8gkxC 8gl0C 8gl4C 8sw2C 8sy4C 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 889.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-NIO / |
#3: Chemical | ChemComp-I77 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
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Crystal grow | Temperature: 298 K / Method: slow cooling / Details: Water/Acetonitrile |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.72925 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72925 Å / Relative weight: 1 |
Reflection | Resolution: 0.964→16.57 Å / Num. obs: 7207 / % possible obs: 86.45 % / Redundancy: 11.7 % / Biso Wilson estimate: 5.41 Å2 / Rmerge(I) obs: 0.08839 / Net I/σ(I): 16.15 |
Reflection shell | Resolution: 0.964→0.9983 Å / Rmerge(I) obs: 0.8479 / Num. unique obs: 183 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→16.57 Å / SU ML: 0.0541 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 19.2729 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: 8.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→16.57 Å
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Refine LS restraints |
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LS refinement shell |
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