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Yorodumi- PDB-1kc2: structure of the triple (Lys(beta)D3Ala, Asp(beta)C8Ala, AspCD2Al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kc2 | ||||||
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Title | structure of the triple (Lys(beta)D3Ala, Asp(beta)C8Ala, AspCD2Ala) mutant of the Src SH2 domain bound to the PQpYEEIPI peptide | ||||||
Components |
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Keywords | TRANSFERASE / SH2 domain / phosphotyrosine | ||||||
Function / homology | Function and homology information osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion ...osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion / phosphorylation / signaling receptor binding / innate immune response / ATP binding Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lubman, O.Y. / Waksman, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Dissection of the energetic coupling across the Src SH2 domain-tyrosyl phosphopeptide interface. Authors: Lubman, O.Y. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kc2.cif.gz | 31.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kc2.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 1kc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kc2 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kc2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 | Mass: 11696.229 Da / Num. of mol.: 1 / Fragment: SH2 domain / Mutation: D190A, D192A, K200A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Production host: Escherichia coli (E. coli) / References: UniProt: P00524, EC: 2.7.1.112 |
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#2: Protein/peptide | Mass: 1068.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. |
#3: Chemical | ChemComp-CO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.79 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 27.9 Å2 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Num. obs: 8048 / % possible obs: 98.4 % / Num. measured all: 166051 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / % possible obs: 97.9 % / Rmerge(I) obs: 0.153 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.29 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 647622.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.2563 Å2 / ksol: 0.352559 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor obs: 0.229 / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.348 / Rfactor Rwork: 0.286 |