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Yorodumi- PDB-4y94: Crystal structure of the PH-TH module of Bruton's tyrosine kinase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y94 | ||||||
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Title | Crystal structure of the PH-TH module of Bruton's tyrosine kinase bound to inositol hexakisphosphate | ||||||
Components | Non-specific protein-tyrosine kinase | ||||||
Keywords | TRANSFERASE / Btk / PH domain / tyrosine kinase / inositol hexakisphosphate | ||||||
Function / homology | Function and homology information FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / DAP12 signaling / B cell affinity maturation / cellular response to interleukin-7 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / negative regulation of cytokine production ...FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / DAP12 signaling / B cell affinity maturation / cellular response to interleukin-7 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / negative regulation of cytokine production / G alpha (q) signalling events / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of B cell proliferation / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / cell maturation / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / T cell receptor signaling pathway / cytoplasmic vesicle / adaptive immune response / intracellular signal transduction / membrane raft / phosphorylation / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Wang, Q. / Kuriyan, J. | ||||||
Citation | Journal: Elife / Year: 2015 Title: Autoinhibition of Bruton's tyrosine kinase (Btk) and activation by soluble inositol hexakisphosphate. Authors: Wang, Q. / Vogan, E.M. / Nocka, L.M. / Rosen, C.E. / Zorn, J.A. / Harrison, S.C. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y94.cif.gz | 146 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y94.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 4y94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y94_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 4y94_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 4y94_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 4y94_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y94 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y94 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 20161.178 Da / Num. of mol.: 4 / Fragment: PH domain (UNP residues 1-170) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: BTK / Production host: Escherichia coli (E. coli) References: UniProt: Q3ZC95, non-specific protein-tyrosine kinase #2: Chemical | ChemComp-IHP / #3: Chemical | ChemComp-ZN / #4: 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: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% PEG 1500, 0.1 M DL-malic acid, 3 mM potasium myo-inositol hexakisphosphate PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.31→50 Å / Num. obs: 30522 / % possible obs: 94.9 % / Redundancy: 2 % / Biso Wilson estimate: 52.82 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.055 / Rrim(I) all: 0.082 / Χ2: 0.987 / Net I/av σ(I): 10.82 / Net I/σ(I): 12.4 / Num. measured all: 61653 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 2.4→46.483 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.84 / Stereochemistry target values: ML
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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 max: 120.62 Å2 / Biso mean: 56.9964 Å2 / Biso min: 24.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→46.483 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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