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Yorodumi- PDB-8dgo: Growth Factor Receptor-Bound Protein 2 (Grb2) bound to phosphoryl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dgo | |||||||||
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Title | Growth Factor Receptor-Bound Protein 2 (Grb2) bound to phosphorylated PEAK3 (pY24) peptide | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / SH2 domain | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Roy, M.J. / Hardy, J.M. / Lucet, I.S. | |||||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling. Authors: Roy, M.J. / Surudoi, M.G. / Kropp, A. / Hou, J. / Dai, W. / Hardy, J.M. / Liang, L.Y. / Cotton, T.R. / Lechtenberg, B.C. / Dite, T.A. / Ma, X. / Daly, R.J. / Patel, O. / Lucet, I.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dgo.cif.gz | 234.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dgo.ent.gz | 157.2 KB | Display | PDB format |
PDBx/mmJSON format | 8dgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dgo_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 8dgo_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 8dgo_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 8dgo_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/8dgo ftp://data.pdbj.org/pub/pdb/validation_reports/dg/8dgo | HTTPS FTP |
-Related structure data
Related structure data | 8dgmC 8dgnC 8dgpC 1griS 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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Unit cell |
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-Components
#1: Protein | Mass: 25384.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q2PG25 #2: Protein/peptide | | Mass: 903.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.66 Å3/Da / Density % sol: 66.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.7 M sodium acetate pH 8.0, 10 % (v/v) glycerol, with 1 mM PEAK3 (pY24) peptide |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2020 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→47.41 Å / Num. obs: 32908 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Net I/σ(I): 11.8 / Num. measured all: 226651 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GRI Resolution: 2.3→41.88 Å / SU ML: 0.3869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0994 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: 73.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→41.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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