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Yorodumi- PDB-1nzl: Crystal Structure of Src SH2 domain bound to doubly phosphorylate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nzl | ||||||
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Title | Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYEpYIPI | ||||||
Components |
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Keywords | TRANSFERASE / SH2 domain / phosphotyrosine | ||||||
Function / homology | Function and homology information osteoclast development / progesterone receptor signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / bone resorption / negative regulation of intrinsic apoptotic signaling pathway / epidermal growth factor receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell adhesion ...osteoclast development / progesterone receptor signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / bone resorption / negative regulation of intrinsic apoptotic signaling pathway / epidermal growth factor receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell adhesion / innate immune response / signaling receptor binding / ATP binding Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Lubman, O.Y. / Waksman, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural and Thermodynamic Basis for the Interaction of the Src SH2 domain with the Activated form of the PDGF beta-receptor Authors: Lubman, O.Y. / Waksman, G. | ||||||
History |
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Remark 600 | HETEROGEN The C8 and O5 atoms of the het hroup PG4 were not modelled and are not present in the coordinates. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nzl.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nzl.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nzl_validation.pdf.gz | 455.8 KB | Display | wwPDB validaton report |
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Full document | 1nzl_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 1nzl_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1nzl_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/1nzl ftp://data.pdbj.org/pub/pdb/validation_reports/nz/1nzl | HTTPS FTP |
-Related structure data
Related structure data | 1nzvC 1spsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11842.352 Da / Num. of mol.: 2 / Fragment: SH2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin) Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: Schmidt-Ruppin / Gene: V-SRC / Plasmid: pET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00524, EC: 2.7.1.112 #2: Protein/peptide | | Mass: 1140.029 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | |
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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: 1.97 Å3/Da / Density % sol: 37 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000,magnesium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 17153 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 10.9 Å2 / Rsym value: 0.069 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 205689 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 1.96 Å / % possible obs: 93.2 % / Rmerge(I) obs: 0.163 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1sps Resolution: 1.9→28.27 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.7867 Å2 / ksol: 0.376681 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. reflection obs: 16447 / % reflection Rfree: 10 % / Rfactor Rfree: 0.263 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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