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- PDB-5e8v: TGF-BETA RECEPTOR TYPE 2 KINASE DOMAIN (E431A,R433A,E485A,K488A,R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5e8v | ||||||
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Title | TGF-BETA RECEPTOR TYPE 2 KINASE DOMAIN (E431A,R433A,E485A,K488A,R493A,R495A) | ||||||
![]() | TGF-beta receptor type-2 | ||||||
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Function / homology | ![]() positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer ...positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sheriff, S. | ||||||
![]() | ![]() Title: Crystal structures of apo and inhibitor-bound TGF beta R2 kinase domain: insights into TGF beta R isoform selectivity. Authors: Tebben, A.J. / Ruzanov, M. / Gao, M. / Xie, D. / Kiefer, S.E. / Yan, C. / Newitt, J.A. / Zhang, L. / Kim, K. / Lu, H. / Kopcho, L.M. / Sheriff, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
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PDB format | ![]() | 54.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5e8sC ![]() 5e8tC ![]() 5e8uC ![]() 5e8wC ![]() 5e8xC ![]() 5e8yC ![]() 5e8zC ![]() 5e90C ![]() 5e91C ![]() 5e92C ![]() 3tzmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35840.680 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 237-549 / Mutation: E431A,R433A,E485A,K488A,R493A,R495A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P37173, ![]() |
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#2: Chemical | ChemComp-GOL / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mm TRIS-HCl, PH 8.5, 150 mm MgCl2, 24%(w/v) PEG4000, 20%(v/v) glcyerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.69→48.04 Å / Num. obs: 40664 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 27.28 Å2 / Rsym value: 0.047 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.69→1.95 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.1 / Rejects: 0 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3TZM Resolution: 1.69→24.74 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.9317 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.092
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Displacement parameters | Biso max: 90.91 Å2 / Biso mean: 31.25 Å2 / Biso min: 15.22 Å2
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Refine analyze | Luzzati coordinate error obs: 0.196 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.69→24.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.73 Å / Total num. of bins used: 20
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