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- PDB-8gbm: 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: 8gbm | ||||||
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Title | Porous framework formed by assembly of a bipyridyl-conjugated helical peptide | ||||||
![]() | LEU-(AIB)-ALA-(AIB)-LEU-CYS-GLN-(AIB)-LEU | ||||||
![]() | DE NOVO PROTEIN | ||||||
Function / homology | ACETATE ION / Chem-I77 / NICOTINIC ACID / LEAD (II) ION![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hess, S.S. / Nguyen, A.I. | ||||||
Funding support | 1items
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![]() | ![]() 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. #1: ![]() Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 18.6 KB | Display | ![]() |
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PDB format | ![]() | 10.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 675.3 KB | Display | ![]() |
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Full document | ![]() | 675.5 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 3.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gb9C ![]() 8gbaC ![]() 8gbhC ![]() 8gbiC ![]() 8gboC ![]() 8gd6C ![]() 8gd8C ![]() 8givC ![]() 8gj7C ![]() 8gk1C ![]() 8gk2C ![]() 8gk9C ![]() 8gkbC ![]() 8gkxC ![]() 8gl0C ![]() 8gl4C ![]() 8gl5C ![]() 8sw2C ![]() 8sy4C 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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Unit cell |
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Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 915.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 8 molecules ![](data/chem/img/NIO.gif)
![](data/chem/img/I77.gif)
![](data/chem/img/PB.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/I77.gif)
![](data/chem/img/PB.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NIO / |
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#3: Chemical | ChemComp-I77 / |
#4: Chemical | ChemComp-PB / |
#5: Chemical | ChemComp-ACT / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.729405 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→15.2 Å / Num. obs: 8046 / % possible obs: 99.67 % / Redundancy: 11.8 % / Biso Wilson estimate: 11.88 Å2 / Rmerge(I) obs: 0.1386 / Net I/σ(I): 8.79 |
Reflection shell | Resolution: 1.04→1.077 Å / Rmerge(I) obs: 1.884 / Num. unique obs: 413 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 13.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→15.2 Å
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Refine LS restraints |
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LS refinement shell |
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