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Yorodumi- PDB-8gji: De novo design of high-affinity protein binders to bioactive heli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gji | |||||||||
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Title | De novo design of high-affinity protein binders to bioactive helical peptides | |||||||||
Components |
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Keywords | DE NOVO PROTEIN / Alpha-helical peptides / protein design / diffusion / deep learning | |||||||||
Function / homology | Function and homology information regulation of insulin secretion / response to activity / hormone activity / glucose homeostasis / extracellular space Similarity search - Function | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | |||||||||
Authors | Torres, S.V. / Leung, P.J.Y. / Bera, A.K. / Baker, D. / Kang, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2024 Title: De novo design of high-affinity binders of bioactive helical peptides. Authors: Vazquez Torres, S. / Leung, P.J.Y. / Venkatesh, P. / Lutz, I.D. / Hink, F. / Huynh, H.H. / Becker, J. / Yeh, A.H. / Juergens, D. / Bennett, N.R. / Hoofnagle, A.N. / Huang, E. / MacCoss, M.J. ...Authors: Vazquez Torres, S. / Leung, P.J.Y. / Venkatesh, P. / Lutz, I.D. / Hink, F. / Huynh, H.H. / Becker, J. / Yeh, A.H. / Juergens, D. / Bennett, N.R. / Hoofnagle, A.N. / Huang, E. / MacCoss, M.J. / Exposit, M. / Lee, G.R. / Bera, A.K. / Kang, A. / De La Cruz, J. / Levine, P.M. / Li, X. / Lamb, M. / Gerben, S.R. / Murray, A. / Heine, P. / Korkmaz, E.N. / Nivala, J. / Stewart, L. / Watson, J.L. / Rogers, J.M. / Baker, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gji.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gji.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/8gji ftp://data.pdbj.org/pub/pdb/validation_reports/gj/8gji | HTTPS FTP |
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-Related structure data
Related structure data | 8gjgC 8t5eC 8t5fC 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
#1: Protein | Mass: 20576.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Protein/peptide | Mass: 3486.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P01273 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 19.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Ammonium chloride 0.1 M Tris pH 8 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→91.93 Å / Num. obs: 13875 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 35.08 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.053 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.81→1.88 Å / Redundancy: 6 % / Rmerge(I) obs: 1.581 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1327 / CC1/2: 0.459 / Rpim(I) all: 0.761 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→45.96 Å / SU ML: 0.2881 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.4549 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→45.96 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.47497523339 Å / Origin y: 3.36439985481 Å / Origin z: 11.5039442839 Å
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Refinement TLS group | Selection details: all |